Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T55703 Target Info
Target Name Plasma retinol-binding protein (RBP4)
Synonyms Retinol-binding protein 4; RBP4; RBP; Plasma retinol-binding protein(1-176); PRBP
Target Type Clinical trial Target
Gene Name RBP4
Biochemical Class Calycin family
UniProt ID
RET4_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Vitamin A Ligand Info
Structure Description Structure of human holo plasma RBP4 PDB:5NU7
Method X-ray diffraction Resolution 1.50 Å Mutation No [1]
PDB Sequence
ERDCRVSSFR
10
VKENFDKARF
20
SGTWYAMAKK
30
DPEGLFLQDN
40
IVAEFSVDET
50

GQMSATAKGR
60
VRLLNNWDVC
70
ADMVGTFTDT
80
EDPAKFKMKY
90
WGVASFLQKG
100

NDDHWIVDTD
110
YDTYAVQYSC
120
RLLNLDGTCA
130
DSYSFVFSRD
140
PNGLPPEAQK
150

IVRQRQEELC
160
LARQYRLIVH
170
NGYCD
Residue
Distance (Å)
LEU35
3.581
PHE36
3.594
LEU37
3.977
ALA43
4.024
PHE45
4.068
ALA55
3.927
THR56
4.429
ALA57
4.095
VAL61
3.720
LEU63
4.470
ALA71
4.657
MET73
3.654
VAL74
4.335
GLY75
4.536
Residue
Distance (Å)
PHE77
4.823
MET88
3.765
TYR90
3.890
PHE96
4.738
LEU97
3.843
GLN98
2.991
ASP102
4.997
HIS104
3.836
GLN117
4.307
ARG121
4.356
TYR133
4.198
PHE135
3.822
PHE137
4.370
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: Tretinoin Ligand Info
Structure Description RETINOL BINDING PROTEIN COMPLEXED WITH TRANSTHYRETIN PDB:1RLB
Method X-ray diffraction Resolution 3.10 Å Mutation No [2]
PDB Sequence
ERDCRVSSFR
10
VKENFDKARF
20
AGTWYAMAKK
30
DPEGLFLQDN
40
IVAEFSVDEN
50

GHMSATAKGR
60
VRLLNNWDVC
70
ADMVGTFTDT
80
EDPAKFKMKY
90
WGVASFLQKG
100

NDDHWIIDTD
110
YETFAVQYSC
120
RLLNLDGTCA
130
DSYSFVFARD
140
PSGFSPQVQK
150

IVRQRQEELC
160
LARQYRLIPH
170
NGYC
Residue
Distance (Å)
LEU35
2.963
PHE36
3.477
LEU37
2.832
ILE41
4.278
ALA43
4.025
PHE45
4.420
ALA55
3.693
THR56
4.536
ALA57
3.359
VAL61
3.633
LEU63
4.129
ALA71
4.764
MET73
3.529
Residue
Distance (Å)
VAL74
4.312
GLY75
4.924
MET88
4.008
TYR90
3.794
LEU97
3.732
GLN98
2.768
ASP102
3.938
HIS104
4.088
GLN117
3.960
TYR133
3.971
PHE135
3.530
PHE137
4.101
Ligand Name: Lauric acid Ligand Info
Structure Description Structure of human urine RBP4 saturated with laurate PDB:5NUA
Method X-ray diffraction Resolution 1.60 Å Mutation No [1]
PDB Sequence
ERDCRVSSFR
10
VKENFDKARF
20
SGTWYAMAKK
30
DPEGLFLQDN
40
IVAEFSVDET
50

GQMSATAKGR
60
VRLLNNWDVC
70
ADMVGTFTDT
80
EDPAKFKMKY
90
WGVASFLQKG
100

NDDHWIVDTD
110
YDTYAVQYSC
120
RLLNLDGTCA
130
DSYSFVFSRD
140
PNGLPPEAQK
150

IVRQRQEELC
160
LARQYRLIVH
170
NGYCD
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DAO or .DAO2 or .DAO3 or :3DAO;style chemicals stick;color identity;select .A:29 or .A:32 or .A:34 or .A:35 or .A:36 or .A:37 or .A:43 or .A:45 or .A:55 or .A:56 or .A:57 or .A:73 or .A:74 or .A:75 or .A:77 or .A:88 or .A:90 or .A:98 or .A:102 or .A:104 or .A:121 or .A:133 or .A:135; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS29
2.930
PRO32
3.526
GLY34
4.864
LEU35
3.767
PHE36
2.916
LEU37
3.029
ALA43
4.888
PHE45
4.565
ALA55
3.661
THR56
4.363
ALA57
3.177
MET73
4.181
Residue
Distance (Å)
VAL74
4.355
GLY75
4.399
PHE77
4.347
MET88
3.513
TYR90
3.748
GLN98
4.419
ASP102
4.735
HIS104
4.368
ARG121
3.768
TYR133
3.841
PHE135
4.037
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: Oleic acid Ligand Info
Structure Description Crystal Structure of RBP4 bound to Oleic Acid PDB:2WQ9
Method X-ray diffraction Resolution 1.65 Å Mutation No [3]
PDB Sequence
ERDCRVSSFR
10
VKENFDKARF
20
SGTWYAMAKK
30
DPEGLFLQDN
40
IVAEFSVDET
50

GQMSATAKGR
60
VRLLNWDVCA
71
DMVGTFTDTE
81
DPAKFKMKYW
91
GVASFLQKGN
101

DDHWIVDTDY
111
DTYAVQYSCR
121
LLNLDGTCAD
131
SYSFVFSRDP
141
NGLPPEAQKI
151

VRQRQEELCL
161
ARQYRLIVHN
171
GYC
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OLA or .OLA2 or .OLA3 or :3OLA;style chemicals stick;color identity;select .A:29 or .A:32 or .A:34 or .A:35 or .A:36 or .A:37 or .A:43 or .A:45 or .A:55 or .A:56 or .A:57 or .A:73 or .A:74 or .A:75 or .A:77 or .A:88 or .A:90 or .A:98 or .A:102 or .A:104 or .A:117 or .A:121 or .A:133 or .A:135 or .A:137; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS29
2.942
PRO32
3.448
GLY34
4.711
LEU35
3.580
PHE36
2.823
LEU37
2.864
ALA43
4.034
PHE45
3.611
ALA55
3.511
THR56
4.045
ALA57
3.768
MET73
3.726
VAL74
3.682
Residue
Distance (Å)
GLY75
3.615
PHE77
4.207
MET88
3.824
TYR90
3.470
GLN98
4.266
ASP102
4.640
HIS104
3.576
GLN117
3.424
ARG121
3.729
TYR133
3.702
PHE135
3.554
PHE137
3.574
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: (1-Benzyl-1h-Imidazol-4-Yl)[4-(2-Chlorophenyl)piperazin-1-Yl]methanone Ligand Info
Structure Description Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with a non-retinoid ligand PDB:4PSQ
Method X-ray diffraction Resolution 2.40 Å Mutation No [4]
PDB Sequence
ERDCRVSSFR
10
VKENFDKARF
20
SGTWYAMAKK
30
DPEGLFLQDN
40
IVAEFSVDET
50

GQMSATAKGR
60
VRLLNNWDVC
70
ADMVGTFTDT
80
EDPAKFKMKY
90
WGVASFLQKG
100

NDDHWIVDTD
110
YDTYAVQYSC
120
RLLNLDGTCA
130
DSYSFVFSRD
140
PNGLPPEAQK
150

IVRQRQEELC
160
LARQYRLIVH
170
NGYCD
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .2WL or .2WL2 or .2WL3 or :32WL;style chemicals stick;color identity;select .B:35 or .B:36 or .B:37 or .B:55 or .B:56 or .B:57 or .B:73 or .B:74 or .B:75 or .B:77 or .B:88 or .B:90 or .B:91 or .B:92 or .B:98 or .B:99 or .B:100 or .B:102 or .B:104 or .B:117 or .B:121 or .B:133 or .B:135; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LEU35
3.700
PHE36
3.099
LEU37
2.975
ALA55
4.100
THR56
4.457
ALA57
3.922
MET73
3.522
VAL74
3.850
GLY75
3.907
PHE77
4.813
MET88
3.586
TYR90
3.275
Residue
Distance (Å)
TRP91
4.374
GLY92
4.581
GLN98
4.728
LYS99
4.002
GLY100
3.501
ASP102
4.289
HIS104
4.020
GLN117
4.924
ARG121
2.815
TYR133
3.737
PHE135
3.754
Ligand Name: 1-[4-(7-Thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(12),2(6),8,10-tetraen-12-yl)piperazin-1-yl]-2-[2-(trifluoromethyl)phenyl]ethanone Ligand Info
Structure Description Crystal structure of Retinol-Binding Protein 4 (RBP4)in complex with a non-retinoid ligand PDB:4O9S
Method X-ray diffraction Resolution 2.30 Å Mutation No [4]
PDB Sequence
ERDCRVSSFR
10
VKENFDKARF
20
SGTWYAMAKK
30
DPEGLFLQDN
40
IVAEFSVDET
50

GQMSATAKGR
60
VRLLNNWDVC
70
ADMVGTFTDT
80
EDPAKFKMKY
90
WGVASFLQKG
100

NDDHWIVDTD
110
YDTYAVQYSC
120
RLLNLDGTCA
130
DSYSFVFSRD
140
PNGLPPEAQK
150

IVRQRQEELC
160
LARQYRLIVH
170
NGYCD
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .2RY or .2RY2 or .2RY3 or :32RY;style chemicals stick;color identity;select .A:35 or .A:36 or .A:37 or .A:43 or .A:45 or .A:55 or .A:56 or .A:57 or .A:61 or .A:71 or .A:73 or .A:74 or .A:75 or .A:77 or .A:88 or .A:90 or .A:96 or .A:102 or .A:104 or .A:117 or .A:121 or .A:133 or .A:135 or .A:137; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LEU35
3.642
PHE36
3.090
LEU37
3.030
ALA43
4.284
PHE45
3.975
ALA55
3.172
THR56
4.062
ALA57
3.561
VAL61
3.730
ALA71
4.793
MET73
3.639
VAL74
3.650
Residue
Distance (Å)
GLY75
3.603
PHE77
4.327
MET88
3.518
TYR90
3.492
PHE96
3.846
ASP102
3.657
HIS104
3.882
GLN117
4.667
ARG121
2.757
TYR133
3.460
PHE135
3.642
PHE137
3.965
Ligand Name: 2-[({4-[2-(Trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid Ligand Info
Structure Description Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand A1120 and engineered binding scaffold PDB:6QBA
Method X-ray diffraction Resolution 1.80 Å Mutation No [5]
PDB Sequence
ERDCRVSSFR
10
VKENFDKARF
20
SGTWYAMAKK
30
DPEGLFLQDN
40
IVAEFSVDET
50

GQMSATAKGR
60
VRLLNNWDVC
70
ADMVGTFTDT
80
EDPAKFKMKY
90
WGVASFLQKG
100

NDDHWIVDTD
110
YDTYAVQYSC
120
RLLNLDGTCA
130
DSYSFVFSRD
140
PNGLPPEAQK
150

IVRQRQEELC
160
LARQYRLIVH
170
NGYCDG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .2T1 or .2T12 or .2T13 or :32T1;style chemicals stick;color identity;select .A:35 or .A:36 or .A:37 or .A:41 or .A:43 or .A:45 or .A:55 or .A:56 or .A:57 or .A:61 or .A:73 or .A:74 or .A:75 or .A:77 or .A:88 or .A:90 or .A:91 or .A:96 or .A:98 or .A:99 or .A:102 or .A:104 or .A:117 or .A:121 or .A:133 or .A:135 or .A:137; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LEU35
2.698
PHE36
2.696
LEU37
2.136
ILE41
4.490
ALA43
4.155
PHE45
3.218
ALA55
2.819
THR56
3.404
ALA57
2.896
VAL61
2.986
MET73
2.653
VAL74
3.189
GLY75
3.077
PHE77
3.343
Residue
Distance (Å)
MET88
2.422
TYR90
1.799
TRP91
4.427
PHE96
2.603
GLN98
2.679
LYS99
4.356
ASP102
3.645
HIS104
2.575
GLN117
4.179
ARG121
2.197
TYR133
2.927
PHE135
2.534
PHE137
3.491
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: (11E,13E,15Z)-octadeca-11,13,15-trienoic acid Ligand Info
Structure Description Structure of the complex of RBP4 with linoleic acid PDB:2WR6
Method X-ray diffraction Resolution 1.80 Å Mutation No [6]
PDB Sequence
ERDCRVSSFR
10
VKENFDKARF
20
SGTWYAMAKK
30
DPEGLFLQDN
40
IVAEFSVDET
50

GQMSATAKGR
60
VRLLNNWDVC
70
ADMVGTFTDT
80
EDPAKFKMKY
90
WGVASFLQKG
100

NDDHWIVDTD
110
YDTYAVQYSC
120
RLLNLDGTCA
130
DSYSFVFSRD
140
PNGLPPEAQK
150

IVRQRQEELC
160
LARQYRLIVH
170
NGYC
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ODT or .ODT2 or .ODT3 or :3ODT;style chemicals stick;color identity;select .A:29 or .A:32 or .A:34 or .A:35 or .A:36 or .A:37 or .A:43 or .A:45 or .A:55 or .A:56 or .A:57 or .A:73 or .A:74 or .A:75 or .A:77 or .A:88 or .A:90 or .A:98 or .A:102 or .A:104 or .A:117 or .A:121 or .A:133 or .A:135 or .A:137; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS29
2.971
PRO32
3.385
GLY34
4.592
LEU35
3.625
PHE36
2.862
LEU37
2.848
ALA43
3.755
PHE45
3.808
ALA55
2.848
THR56
3.447
ALA57
3.808
MET73
3.831
VAL74
3.626
Residue
Distance (Å)
GLY75
3.706
PHE77
4.057
MET88
3.699
TYR90
3.517
GLN98
4.425
ASP102
4.765
HIS104
3.751
GLN117
3.748
ARG121
3.728
TYR133
3.860
PHE135
3.804
PHE137
3.570
References  Top
REF 1 Human plasma retinol-binding protein (RBP4) is also a fatty acid-binding protein. Biochim Biophys Acta Mol Cell Biol Lipids. 2018 Apr;1863(4):458-466.
REF 2 Structure of a complex of two plasma proteins: transthyretin and retinol-binding protein. Science. 1995 May 19;268(5213):1039-41.
REF 3 Crystal Structure of Rbp4 Bound to Oleic Acid
REF 4 Structure-assisted discovery of the first non-retinoid ligands for Retinol-Binding Protein 4. Bioorg Med Chem Lett. 2014 Jul 1;24(13):2885-91.
REF 5 A conformation-specific ON-switch for controlling CAR T cells with an orally available drug. Proc Natl Acad Sci U S A. 2020 Jun 30;117(26):14926-14935.
REF 6 Identification of a Non-Retinoid Compound and Fatty Acids as Ligands for Retinol Binding Protein 4 and Their Implications in Diabetes

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