Structure of PDB 3kl6 Chain A Binding Site BS01

Receptor Information
>3kl6 Chain A (length=232) 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
GIVSWGEGCARKGKYGIYTKVTAFLKWIDRSM
Ligand information
Ligand ID443
InChIInChI=1S/C22H26ClN3O5S/c23-17-4-2-16-13-19(5-3-15(16)12-17)32(30,31)14-20(27)21(28)25-10-6-18(7-11-25)26-9-1-8-24-22(26)29/h2-5,12-13,18,20,27H,1,6-11,14H2,(H,24,29)/t20-/m1/s1
InChIKeyGEHAEMCVKDPMKO-HXUWFJFHSA-N
SMILES
SoftwareSMILES
CACTVS 3.352O[C@H](C[S](=O)(=O)c1ccc2cc(Cl)ccc2c1)C(=O)N3CC[C@@H](CC3)N4CCCNC4=O
OpenEye OEToolkits 1.7.0c1cc(cc2c1cc(cc2)Cl)S(=O)(=O)C[C@H](C(=O)N3CCC(CC3)N4CCCNC4=O)O
CACTVS 3.352O[CH](C[S](=O)(=O)c1ccc2cc(Cl)ccc2c1)C(=O)N3CC[CH](CC3)N4CCCNC4=O
OpenEye OEToolkits 1.7.0c1cc(cc2c1cc(cc2)Cl)S(=O)(=O)CC(C(=O)N3CCC(CC3)N4CCCNC4=O)O
FormulaC22 H26 Cl N3 O5 S
Name1-(1-{(2S)-3-[(6-chloronaphthalen-2-yl)sulfonyl]-2-hydroxypropanoyl}piperidin-4-yl)tetrahydropyrimidin-2(1H)-one
ChEMBLCHEMBL1095032
DrugBankDB11984
ZINCZINC000013986542
PDB chain3kl6 Chain A 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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PDB3kl6 Discovery of a tetrahydropyrimidin-2(1H)-one derivative (TAK-442) as a potent, selective, and orally active factor Xa inhibitor.
Resolution1.45 Å
Binding residue
(original residue number in PDB)		E97 T98 F174 D189 A190 Q192 S195 V213 S214 W215 G216 G219 C220 G226 I227 Y228
Binding residue
(residue number reindexed from 1)		E83 T84 F162 D179 A180 Q182 S185 V203 S204 W205 G206 G208 C209 G216 I217 Y218
Annotation score1
Binding affinityMOAD: ic50=3.5nM
PDBbind-CN: -logKd/Ki=8.46,IC50=3.5nM
BindingDB: IC50=3.5nM,Ki=1.8nM
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:3kl6, PDBe:3kl6, PDBj:3kl6
PDBsum3kl6
PubMed20355714
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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