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Structure of PDB 1ygc Chain H Binding Site BS02

Receptor Information
>1ygc Chain H (length=254) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWR
NLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPV
VLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNV
PRLMTQDCLQQSRKVGDSPNITEYMFCAGYSDGSKDSCKGDSGGPHATHY
RGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLR
APFP
Ligand information
Ligand ID905
InChIInChI=1S/C25H28FN5O6S/c1-3-36-16-12-19(22(26)21(13-16)37-4-2)23(30-15-8-9-18(24(28)29)20(32)11-15)25(33)31-38(34,35)17-7-5-6-14(27)10-17/h5-13,23,30,32H,3-4,27H2,1-2H3,(H3,28,29)(H,31,33)/t23-/m1/s1
InChIKeyMLPXCKVDBGAVRJ-HSZRJFAPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCOc1cc(OCC)c(F)c(c1)[CH](Nc2ccc(C(N)=N)c(O)c2)C(=O)N[S](=O)(=O)c3cccc(N)c3
OpenEye OEToolkits 1.5.0[H]N=C(c1ccc(cc1O)NC(c2cc(cc(c2F)OCC)OCC)C(=O)NS(=O)(=O)c3cccc(c3)N)N
CACTVS 3.341CCOc1cc(OCC)c(F)c(c1)[C@@H](Nc2ccc(C(N)=N)c(O)c2)C(=O)N[S](=O)(=O)c3cccc(N)c3
ACDLabs 10.04O=S(=O)(c1cccc(N)c1)NC(=O)C(c2cc(OCC)cc(OCC)c2F)Nc3ccc(C(=[N@H])N)c(O)c3
OpenEye OEToolkits 1.5.0[H]/N=C(/c1ccc(cc1O)N[C@H](c2cc(cc(c2F)OCC)OCC)C(=O)NS(=O)(=O)c3cccc(c3)N)\N
FormulaC25 H28 F N5 O6 S
Name(R)-4-[2-(3-AMINO-BENZENESULFONYLAMINO)-1-(3,5-DIETHOXY-2-FLUOROPHENYL)-2-OXO-ETHYLAMINO]-2-HYDROXY-BENZAMIDINE
ChEMBLCHEMBL1230642
DrugBank
ZINCZINC000012338906
PDB chain1ygc Chain H Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1ygc A selective, slow binding inhibitor of factor VIIa binds to a nonstandard active site conformation and attenuates thrombus formation in vivo.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		H57 T99 D102 D189 S190 K192 S195 V213 S214 W215 G216 G219 C220
Binding residue
(residue number reindexed from 1)		H41 T87 D90 D186 S187 K189 S192 V210 S211 W212 G213 G215 C216
Annotation score1
Binding affinityMOAD: Ki=0.35nM
BindingDB: Ki=0.35nM
Enzymatic activity
Enzyme Commision number 3.4.21.21: coagulation factor VIIa.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:1ygc, PDBe:1ygc, PDBj:1ygc
PDBsum1ygc
PubMed15632123
UniProtP08709|FA7_HUMAN Coagulation factor VII (Gene Name=F7)

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