Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T43332 Target Info
Target Name Coagulation factor VII (F7)
Synonyms Serum prothrombin conversion accelerator; SPCA; Proconvertin; Eptacog alfa
Target Type Successful Target
Gene Name F7
Biochemical Class Peptidase
UniProt ID
FA7_HUMAN
Ligand General Information  Top
Ligand Name Beta-D-Glucose Ligand Info
Canonical SMILES C(C1C(C(C(C(O1)O)O)O)O)O
InChI 1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6-/m1/s1
InChIKey WQZGKKKJIJFFOK-VFUOTHLCSA-N
PubChem Compound ID 64689
Drug Binding Sites of Target  Top
PDB ID: 3TH2      Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological Ca2+
Method X-ray diffraction Resolution 1.72 Å Mutation No [1]
PDB Sequence
ANAFLLRPGS
12
LRCKQCSFAR
28
IFKDARTKLF
40
WISYSDGDQC
50
ASSPCQNGGS
60

CKDQLQSYIC
70
FCLPAFEGRN
80
CETHKDDQLI
90
CVNENGGCEQ
100
YCSDHTGTKR
110

SCRCHEGYSL
120
LADGVSCTPT
130
VEYPCGKIPI
140
LE
Residue
Distance (Å)
GLN49
2.581
CYS50
4.762
SER52
1.437
Residue
Distance (Å)
SER53
4.933
PRO54
4.108
TYR68
3.314
PDB ID: 3TH4      Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological Ca2+
Method X-ray diffraction Resolution 1.80 Å Mutation No [2]
PDB Sequence
ANAFLLRPGS
12
LRCKQCSFAR
28
IFKDARTKLF
40
WISYSDGDQC
50
ASSPCQNGGS
60

CKDQLQSYIC
70
FCLPAFEGRN
80
CETHKDDQLI
90
CVNENGGCEQ
100
YCSDHTGTKR
110

SCRCHEGYSL
120
LADGVSCTPT
130
VEYPCGKIPI
140
LE
Residue
Distance (Å)
GLN49
3.203
SER52
1.453
SER53
4.978
Residue
Distance (Å)
PRO54
3.778
TYR68
3.495
PDB ID: 4IBL      Rubidium Sites in Blood Coagulation Factor VIIa
Method X-ray diffraction Resolution 1.80 Å Mutation No [3]
PDB Sequence
AFLLRPGSLR
15
CKQCSFARIF
31
KDARTKLFWI
42
SYSDGDQCAS
52
SPCQNGGSCK
62

DQLQSYICFC
72
LPAFEGRNCE
82
THKDDQLICV
92
NENGGCEQYC
102
SDHTGTKRSC
112

RCHEGYSLLA
122
DGVSCTPTVE
132
YPCGKIPILE
142
Residue
Distance (Å)
GLN49
2.862
SER52
1.461
Residue
Distance (Å)
PRO54
3.643
TYR68
3.304
PDB ID: 1DAN      Complex of active site inhibited human blood coagulation factor VIIA with human recombinant soluble tissue factor
Method X-ray diffraction Resolution 2.00 Å Mutation No [4]
PDB Sequence
ANAFLLRPGS
12
LRCKQCSFAR
28
IFKDARTKLF
40
WISYSDGDQC
50
ASSPCQNGGS
60

CKDQLQSYIC
70
FCLPAFEGRN
80
CETHKDDQLI
90
CVNENGGCEQ
100
YCSDHTGTKR
110

SCRCHEGYSL
120
LADGVSCTPT
130
VEYPCGKIPI
140
LE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .L:49 or .L:52 or .L:53 or .L:54 or .L:68; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN49
3.170
SER52
1.442
SER53
4.820
Residue
Distance (Å)
PRO54
3.818
TYR68
3.808
PDB ID: 2PUQ      Crystal structure of active site inhibited coagulation factor VIIA in complex with soluble tissue factor
Method X-ray diffraction Resolution 2.05 Å Mutation No [5]
PDB Sequence
QCASSPCQNG
58
GSCKDQLQSY
68
ICFCLPAFEG
78
RNCETHKDDQ
88
LICVNENGGC
98

EQYCSDHTGT
108
KRSCRCHEGY
118
SLLADGVSCT
128
PTVEYPCGKI
138
PILE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .L:49 or .L:50 or .L:51 or .L:52 or .L:53 or .L:54 or .L:68; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN49
1.990
CYS50
4.046
ALA51
4.014
SER52
1.329
Residue
Distance (Å)
SER53
4.837
PRO54
3.918
TYR68
4.542
PDB ID: 1WTG      Human Factor Viia-Tissue Factor Complexed with ethylsulfonamide-D-biphenylalanine-Gln-p-aminobenzamidine
Method X-ray diffraction Resolution 2.20 Å Mutation Yes [6]
PDB Sequence
ANAFLLRPGS
12
LRCKQCSFAR
28
IFKDARTKLF
40
WISYSDGDQC
50
ASSPCQNGGS
60

CKDQLQSYIC
70
FCLPAFEGRN
80
CETHKDDQLI
90
CVNENGGCEQ
100
YCSDHTGTKR
110

SCRCHEGYSL
120
LADGVSCTPT
130
VEYPCGKIPI
140
LE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .L:49 or .L:51 or .L:52 or .L:53 or .L:54 or .L:68; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN49
3.037
ALA51
4.987
SER52
1.442
Residue
Distance (Å)
SER53
4.789
PRO54
3.401
TYR68
3.562
PDB ID: 2ZWL      Human factor viia-tissue factor complexed with highly selective peptide inhibitor
Method X-ray diffraction Resolution 2.20 Å Mutation No [7]
PDB Sequence
ANAFLLRPGS
12
LRCKQCSFAR
28
IFKDARTKLF
40
WISYSDGDQC
50
ASSPCQNGGS
60

CKDQLQSYIC
70
FCLPAFEGRN
80
CETHKDDQLI
90
CVNENGGCEQ
100
YCSDHTGTKR
110

SCRCHEGYSL
120
LADGVSCTPT
130
VEYPCGKIPI
140
LE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .L:49 or .L:52 or .L:53 or .L:54 or .L:68; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN49
3.221
SER52
1.436
SER53
4.553
Residue
Distance (Å)
PRO54
3.675
TYR68
3.515
PDB ID: 1WUN      Human Factor Viia-Tissue Factor Complexed with ethylsulfonamide-D-Trp-Gln-p-aminobenzamidine
Method X-ray diffraction Resolution 2.40 Å Mutation Yes [8]
PDB Sequence
ANAFLLRPGS
12
LRCKQCSFAR
28
IFKDARTKLF
40
WISYSDGDQC
50
ASSPCQNGGS
60

CKDQLQSYIC
70
FCLPAFEGRN
80
CETHKDDQLI
90
CVNENGGCEQ
100
YCSDHTGTKR
110

SCRCHEGYSL
120
LADGVSCTPT
130
VEYPCGKIPI
140
LE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .L:49 or .L:52 or .L:53 or .L:54 or .L:68; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN49
2.994
SER52
1.442
SER53
4.910
Residue
Distance (Å)
PRO54
3.426
TYR68
3.738
PDB ID: 1W0Y      tf7a_3771 complex
Method X-ray diffraction Resolution 2.50 Å Mutation No [9]
PDB Sequence
ANAFLLRPGS
12
LRCKQCSFAR
28
IFKDAERTKL
39
FWISYSDGDQ
49
CASSPCQNGG
59

SCKDQLQSYI
69
CFCLPAFEGR
79
NCETHKDDQL
89
ICVNENGGCE
99
QYCSDHTGTK
109

RSCRCHEGYS
119
LLADGVSCTP
129
TVEYPCGKIP
139
ILE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .L:49 or .L:52 or .L:53 or .L:54 or .L:68; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN49
2.964
SER52
1.427
SER53
4.758
Residue
Distance (Å)
PRO54
3.754
TYR68
3.710
PDB ID: 1WQV      Human Factor Viia-Tissue Factor Complexed with propylsulfonamide-D-Thr-Met-p-aminobenzamidine
Method X-ray diffraction Resolution 2.50 Å Mutation No [10]
PDB Sequence
ANAFLLRPGS
12
LRCKQCSFAR
28
IFKDARTKLF
40
WISYSDGDQC
50
ASSPCQNGGS
60

CKDQLQSYIC
70
FCLPAFEGRN
80
CETHKDDQLI
90
CVNENGGCEQ
100
YCSDHTGTKR
110

SCRCHEGYSL
120
LADGVSCTPT
130
VEYPCGKIPI
140
LE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .L:49 or .L:52 or .L:54 or .L:67 or .L:68; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN49
3.106
SER52
1.441
PRO54
3.737
Residue
Distance (Å)
SER67
4.857
TYR68
3.627
PDB ID: 2ZZU      Human Factor VIIA-Tissue Factor Complexed with ethylsulfonamide-D-5-(3-carboxybenzyloxy)-Trp-Gln-p-aminobenzamidine
Method X-ray diffraction Resolution 2.50 Å Mutation No [11]
PDB Sequence
ANAFLLRPGS
12
LRCKQCSFAR
28
IFKDARTKLF
40
WISYSDGDQC
50
ASSPCQNGGS
60

CKDQLQSYIC
70
FCLPAFEGRN
80
CETHKDDQLI
90
CVNENGGCEQ
100
YCSDHTGTKR
110

SCRCHEGYSL
120
LADGVSCTPT
130
VEYPCGKIPI
140
LE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .L:49 or .L:52 or .L:53 or .L:54 or .L:67 or .L:68; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN49
3.132
SER52
1.438
SER53
4.824
Residue
Distance (Å)
PRO54
3.778
SER67
4.874
TYR68
3.491
PDB ID: 1WSS      Human Factor Viia-Tissue Factor in Complex with peptide-mimetic inhibitor that has two charged groups in P2 and P4
Method X-ray diffraction Resolution 2.60 Å Mutation No [12]
PDB Sequence
ANAFLLRPGS
12
LRCKQCSFAR
28
IFKDARTKLF
40
WISYSDGDQC
50
ASSPCQNGGS
60

CKDQLQSYIC
70
FCLPAFEGRN
80
CETHKDDQLI
90
CVNENGGCEQ
100
YCSDHTGTKR
110

SCRCHEGYSL
120
LADGVSCTPT
130
VEYPCGKIPI
140
LE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .L:49 or .L:52 or .L:54 or .L:68; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN49
3.403
SER52
1.443
Residue
Distance (Å)
PRO54
3.748
TYR68
3.526
PDB ID: 1WV7      Human Factor Viia-Tissue Factor Complexed with ethylsulfonamide-D-5-propoxy-Trp-Gln-p-aminobenzamidine
Method X-ray diffraction Resolution 2.70 Å Mutation Yes [8]
PDB Sequence
ANAFLLRPGS
12
LRCKQCSFAR
28
IFKDARTKLF
40
WISYSDGDQC
50
ASSPCQNGGS
60

CKDQLQSYIC
70
FCLPAFEGRN
80
CETHKDDQLI
90
CVNENGGCEQ
100
YCSDHTGTKR
110

SCRCHEGYSL
120
LADGVSCTPT
130
VEYPCGKIPI
140
LE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .L:49 or .L:52 or .L:53 or .L:54 or .L:68; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN49
3.152
SER52
1.440
SER53
4.811
Residue
Distance (Å)
PRO54
3.760
TYR68
3.457
PDB ID: 2ZP0      Human factor viia-tissue factor complexed with benzylsulfonamide-D-ile-gln-P-aminobenzamidine
Method X-ray diffraction Resolution 2.70 Å Mutation No [13]
PDB Sequence
ANAFLLRPGS
12
LRCKQCSFAR
28
IFKDARTKLF
40
WISYSDGDQC
50
ASSPCQNGGS
60

CKDQLQSYIC
70
FCLPAFEGRN
80
CETHKDDQLI
90
CVNENGGCEQ
100
YCSDHTGTKR
110

SCRCHEGYSL
120
LADGVSCTPT
130
VEYPCGKIPI
140
LE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .L:49 or .L:52 or .L:53 or .L:54 or .L:66 or .L:67 or .L:68; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN49
3.240
SER52
1.440
SER53
4.981
PRO54
4.084
Residue
Distance (Å)
GLN66
4.944
SER67
4.781
TYR68
3.768
PDB ID: 3TH3      Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological Ca2+
Method X-ray diffraction Resolution 2.70 Å Mutation No [14]
PDB Sequence
GDQCASSPCQ
56
NGGSCKDQLQ
66
SYICFCLPAF
76
EGRNCETHKD
86
DQLICVNENG
96

GCEQYCSDHT
106
GTKRSCRCHE
116
GYSLLADGVS
126
CTPTVEYPCG
136
KIPILE
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Residue
Distance (Å)
GLN49
3.103
SER52
1.446
SER53
4.106
Residue
Distance (Å)
PRO54
2.986
TYR68
3.576
PDB ID: 1W2K      tf7a_4380 complex
Method X-ray diffraction Resolution 3.00 Å Mutation No [9]
PDB Sequence
ANAFLLRPGS
12
LRCKQCSFAR
28
IFKDAERTKL
39
FWISYSDGDQ
49
CASSPCQNGG
59

SCKDQLQSYI
69
CFCLPAFEGR
79
NCETHKDDQL
89
ICVNENGGCE
99
QYCSDHTGTK
109

RSCRCHEGYS
119
LLADGVSCTP
129
TVEYPCGKIP
139
ILE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .L:49 or .L:52 or .L:53 or .L:54 or .L:68; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN49
3.146
SER52
1.416
SER53
4.918
Residue
Distance (Å)
PRO54
3.923
TYR68
3.586
PDB ID: 4Z6A      Crystal Structure of a FVIIa-Trypsin Chimera (YT) in Complex with Soluble Tissue Factor
Method X-ray diffraction Resolution 2.25 Å Mutation Yes [15]
PDB Sequence
DQCASSPCQN
57
GGSCKDQLQS
67
YICFCLPAFE
77
GRNCETHKDD
87
QLICVNENGG
97

CEQYCSDHTK
109
RSCRCHEGYS
119
LLADGVSCTP
129
TVEYPCGKIP
139
ILEK
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .L:49 or .L:50 or .L:51 or .L:52 or .L:53 or .L:54 or .L:67 or .L:68 or .L:79 or .L:80; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN49
2.255
CYS50
4.332
ALA51
4.771
SER52
2.133
SER53
4.795
Residue
Distance (Å)
PRO54
3.049
SER67
4.630
TYR68
1.954
ARG79
4.132
ASN80
3.994
PDB ID: 4ZMA      Crystal Structure of a FVIIa-Trypsin Chimera (ST) in Complex with Soluble Tissue Factor
Method X-ray diffraction Resolution 2.30 Å Mutation Yes [15]
PDB Sequence
ANAFLLRPGS
12
LRCKQCSFAR
28
IFKDARTKLF
40
WISYSDGDQC
50
ASSPCQNGGS
60

CKDQLQSYIC
70
FCLPAFEGRN
80
CETHKDDQLI
90
CVNENGGCEQ
100
YCSDHKRSCR
113

CHEGYSLLAD
123
GVSCTPTVEY
133
PCGKIPILEK
143
R
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .L:48 or .L:49 or .L:50 or .L:51 or .L:52 or .L:53 or .L:54 or .L:68 or .L:80; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASP48
4.476
GLN49
2.239
CYS50
4.219
ALA51
3.827
SER52
1.374
Residue
Distance (Å)
SER53
4.756
PRO54
2.567
TYR68
2.554
ASN80
4.097
References  Top
REF 1 Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla)
REF 2 Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla)
REF 3 Structure of human factor VIIa-soluble tissue factor with calcium, magnesium and rubidium. doi:10.1107/S2059798321003922.
REF 4 The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor. Nature. 1996 Mar 7;380(6569):41-6.
REF 5 Engineering the substrate and inhibitor specificities of human coagulation Factor VIIa. Biochem J. 2007 Aug 1;405(3):429-38.
REF 6 Novel interactions of large P3 moiety and small P4 moiety in the binding of the peptide mimetic factor VIIa inhibitor. Biochem Biophys Res Commun. 2005 Jan 28;326(4):859-65.
REF 7 Human factor viia-tissue factor complexed with highly selective peptide inhibitor
REF 8 Structure-based design of P3 moieties in the peptide mimetic factor VIIa inhibitor. Biochem Biophys Res Commun. 2005 Feb 11;327(2):589-96.
REF 9 Design of selective phenylglycine amide tissue factor/factor VIIa inhibitors. Bioorg Med Chem Lett. 2005 Feb 1;15(3):817-22.
REF 10 Crystal structure of human factor VIIa/tissue factor in complex with peptide mimetic inhibitor. Biochem Biophys Res Commun. 2004 Nov 26;324(4):1227-33.
REF 11 Design and synthesis of peptidomimetic factor VIIa inhibitors. Chem Pharm Bull (Tokyo). 2010 Jan;58(1):38-44.
REF 12 Structure of human factor VIIa/tissue factor in complex with a peptide-mimetic inhibitor: high selectivity against thrombin by introducing two charged groups in P2 and P4. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Feb 1;61(Pt 2):169-73.
REF 13 Peptide Mimetic Factor VIIa Inhibitor: Importance of Hydrophilic Pocket in S2 Site to Improve Selectivity aganist Thrombin
REF 14 Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla)
REF 15 Molecular Basis of Enhanced Activity in Factor VIIa-Trypsin Variants Conveys Insights into Tissue Factor-mediated Allosteric Regulation of Factor VIIa Activity. J Biol Chem. 2016 Feb 26;291(9):4671-83.

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