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 T80975 Target Info
Target Name Vascular endothelial growth factor receptor 2 (KDR)
Synonyms VEGFR2; VEGFR-2; VEGF-2 receptor; Protein-tyrosine kinase receptor flk-1; Kinase insert domain receptor; Fetal liver kinase 1; FLK1; FLK-1; CD309
Target Type Successful Target
Gene Name KDR
Biochemical Class Kinase
UniProt ID
VGFR2_HUMAN
Ligand General Information  Top
Ligand Name Sorafenib Ligand Info
Canonical SMILES CNC(=O)C1=NC=CC(=C1)OC2=CC=C(C=C2)NC(=O)NC3=CC(=C(C=C3)Cl)C(F)(F)F
InChI 1S/C21H16ClF3N4O3/c1-26-19(30)18-11-15(8-9-27-18)32-14-5-2-12(3-6-14)28-20(31)29-13-4-7-17(22)16(10-13)21(23,24)25/h2-11H,1H3,(H,26,30)(H2,28,29,31)
InChIKey MLDQJTXFUGDVEO-UHFFFAOYSA-N
PubChem Compound ID 216239
Drug Binding Sites of Target  Top
PDB ID: 4ASD      Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with SORAFENIB (BAY 43-9006)
Method X-ray diffraction Resolution 2.03 Å Mutation Yes [1]
PDB Sequence
DPDELPLDEH
816
CERLPYDASK
826
WEFPRDRLKL
836
GKPLGRGAFG
846
QVIEADAFGI
856

DKTATCRTVA
866
VKMLKEGATH
876
SEHRALMSEL
886
KILIHIGHHL
896
NVVNLLGACT
906

KPGGPLMVIV
916
EFCKFGNLST
926
YLRSKRNEFV
936
PYYKDFLTLE
1003
HLICYSFQVA
1013

KGMEFLASRK
1023
CIHRDLAARN
1033
ILLSEKNVVK
1043
ICDFGLARDI
1053
YKDPDYVRKG
1063

DARLPLKWMA
1073
PETIFDRVYT
1083
IQSDVWSFGV
1093
LLWEIFSLGA
1103
SPYPGVKIDE
1113

EFCRRLKEGT
1123
RMRAPDYTTP
1133
EMYQTMLDCW
1143
HGEPSQRPTF
1153
SELVEHLGNL
1163

LQANA
Residue
Distance (Å)
LEU840
3.528
VAL848
3.277
ALA866
3.487
LYS868
3.485
GLU885
2.581
ILE888
4.235
LEU889
3.602
ILE892
3.885
VAL898
4.474
VAL899
3.326
VAL916
3.509
GLU917
3.170
PHE918
3.489
Residue
Distance (Å)
CYS919
2.881
LYS920
3.708
PHE921
4.591
GLY922
3.698
LEU1019
3.295
ILE1025
4.340
HIS1026
3.379
LEU1035
3.525
ILE1044
2.994
CYS1045
3.226
ASP1046
2.794
PHE1047
3.399
PDB ID: 3WZE      KDR in complex with ligand sorafenib
Method X-ray diffraction Resolution 1.90 Å Mutation Yes [2]
PDB Sequence
EHCERLPYDA
824
SKWEFPRDRL
834
KLGKPLGRGA
844
FGQVIEADAF
854
GIDKTATCRT
864

VAVKMLKEGA
874
THSEHRALMS
884
ELKILIHIGH
894
HLNVVNLLGA
904
CTKPGGPLMV
914

IVEFCKFGNL
924
STYLRSKRNE
934
FVPYKDLYKD
998
FLTLEHLICY
1008
SFQVAKGMEF
1018

LASRKCIHRD
1028
LAARNILLSE
1038
KNVVKICDFG
1048
LARDIYKDPD
1058
YVRKGARLPL
1069

KWMAPETIFD
1079
RVYTIQSDVW
1089
SFGVLLWEIF
1099
SLGASPYPGV
1109
KIDEEFCRRL
1119

KEGTRMRAPD
1129
YTTPEMYQTM
1139
LDCWHGEPSQ
1149
RPTFSELVEH
1159
LGNLLQAN
Residue
Distance (Å)
LEU840
3.643
VAL848
3.320
ALA866
3.467
LYS868
3.736
GLU885
2.698
ILE888
4.204
LEU889
3.744
ILE892
3.651
VAL898
3.658
VAL899
3.378
VAL916
3.533
GLU917
3.279
PHE918
3.509
Residue
Distance (Å)
CYS919
2.756
LYS920
3.618
PHE921
4.540
GLY922
3.712
LEU1019
3.718
ILE1025
4.713
HIS1026
3.248
LEU1035
3.715
ILE1044
3.118
CYS1045
3.279
ASP1046
2.834
PHE1047
3.471
References  Top
REF 1 Molecular conformations, interactions, and properties associated with drug efficiency and clinical performance among VEGFR TK inhibitors. Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18281-9.
REF 2 Distinct binding mode of multikinase inhibitor lenvatinib revealed by biochemical characterization. ACS Med Chem Lett. 2014 Nov 17;6(1):89-94.

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