Structure of PDB 1fax Chain A Binding Site BS02

Receptor Information
>1fax Chain A (length=235) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRF
KVRVGDRNTAAEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITF
RMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPY
VDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVT
GIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTR
Ligand information
Ligand IDDX9
InChIInChI=1S/C26H28N4O3/c1-16(27)30-11-10-23(15-30)33-22-8-6-19(7-9-22)24(26(31)32)13-17-2-3-18-4-5-20(25(28)29)14-21(18)12-17/h2-9,12,14,23-24,27H,10-11,13,15H2,1H3,(H3,28,29)(H,31,32)/b27-16+/t23-,24-/m0/s1
InChIKeyAGRCGQSFFMCBRE-DGUCVARSSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(c2ccc(OC1CCN(C(=[N@H])C)C1)cc2)Cc4cc3cc(C(=[N@H])N)ccc3cc4
OpenEye OEToolkits 1.5.0[H]/N=C(\C)/N1CC[C@@H](C1)Oc2ccc(cc2)[C@H](Cc3ccc4ccc(cc4c3)/C(=N/[H])/N)C(=O)O
CACTVS 3.341CC(=N)N1CC[CH](C1)Oc2ccc(cc2)[CH](Cc3ccc4ccc(cc4c3)C(N)=N)C(O)=O
CACTVS 3.341CC(=N)N1CC[C@@H](C1)Oc2ccc(cc2)[C@H](Cc3ccc4ccc(cc4c3)C(N)=N)C(O)=O
OpenEye OEToolkits 1.5.0[H]N=C(C)N1CCC(C1)Oc2ccc(cc2)C(Cc3ccc4ccc(cc4c3)C(=N[H])N)C(=O)O
FormulaC26 H28 N4 O3
Name(2S)-3-(7-carbamimidoylnaphthalen-2-yl)-2-[4-({(3R)-1-[(1Z)-ethanimidoyl]pyrrolidin-3-yl}oxy)phenyl]propanoic acid;
DX9056A
ChEMBL
DrugBank
ZINC
PDB chain1fax Chain A Residue 265 [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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PDB1fax X-ray structure of active site-inhibited clotting factor Xa. Implications for drug design and substrate recognition.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		E97 D189 A190 C191 Q192 W215 G216 G218
Binding residue
(residue number reindexed from 1)		E83 D179 A180 C181 Q182 W205 G206 G208
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.39,Ki=41nM
BindingDB: Ki=41nM,IC50=70nM
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:1fax, PDBe:1fax, PDBj:1fax
PDBsum1fax
PubMed8939944
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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