Structure of PDB 1xkb Chain D Binding Site BS02

Receptor Information
>1xkb Chain D (length=234) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRF
KVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITF
RMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPY
VDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVT
GIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKT
Ligand information
Ligand ID4PP
InChIInChI=1S/C23H24N4O2/c24-22(25)19-7-2-5-17(15-19)16-4-1-6-18(14-16)21(23(28)29)8-3-11-27-20-9-12-26-13-10-20/h1-2,4-7,9-10,12-15,21H,3,8,11H2,(H3,24,25)(H,26,27)(H,28,29)/t21-/m0/s1
InChIKeyFJEAIYBDDQAFGU-NRFANRHFSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=N)c1cccc(c1)c2cccc(c2)[C@H](CCCNc3ccncc3)C(O)=O
ACDLabs 10.04O=C(O)C(c2cccc(c1cc(C(=[N@H])N)ccc1)c2)CCCNc3ccncc3
OpenEye OEToolkits 1.5.0c1cc(cc(c1)[C@H](CCCNc2ccncc2)C(=O)O)c3cccc(c3)C(=N)N
OpenEye OEToolkits 1.5.0c1cc(cc(c1)C(CCCNc2ccncc2)C(=O)O)c3cccc(c3)C(=N)N
CACTVS 3.341NC(=N)c1cccc(c1)c2cccc(c2)[CH](CCCNc3ccncc3)C(O)=O
FormulaC23 H24 N4 O2
Name(2S)-(3'-AMIDINO-3-BIPHENYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID
ChEMBLCHEMBL105532
DrugBank
ZINCZINC000003815585
PDB chain1xkb Chain D Residue 999 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1xkb Structural basis for chemical inhibition of human blood coagulation factor Xa.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		T98 Y99 F174 D189 A190 C191 Q192 S195 V213 W215 G216 G218
Binding residue
(residue number reindexed from 1)		T84 Y85 F162 D179 A180 C181 Q182 S185 V203 W205 G206 G208
Annotation score1
Binding affinityMOAD: Ki=131nM
BindingDB: IC50=270nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 Q192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H42 D88 Q182 G183 D184 S185 G186
Enzyme Commision number 3.4.21.6: coagulation factor Xa.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function
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Biological Process
External links
PDB RCSB:1xkb, PDBe:1xkb, PDBj:1xkb
PDBsum1xkb
PubMed9618463
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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