Structure of PDB 4ax9 Chain H Binding Site BS03

Receptor Information
>4ax9 Chain H (length=250) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
Ligand information
Ligand IDN5N
InChIInChI=1S/C26H34N6O6S/c27-26(28)31-11-3-4-17(15-31)14-29-23(33)13-22(25(36)32(16-24(34)35)20-8-9-20)30-39(37,38)21-10-7-18-5-1-2-6-19(18)12-21/h1-2,5-7,10,12,17,20,22,30H,3-4,8-9,11,13-16H2,(H3,27,28)(H,29,33)(H,34,35)/t17-,22-/m0/s1
InChIKeyBYDKEYCXCIVOOV-JTSKRJEESA-N
SMILES
SoftwareSMILES
CACTVS 3.370NC(=N)N1CCC[CH](CNC(=O)C[CH](N[S](=O)(=O)c2ccc3ccccc3c2)C(=O)N(CC(O)=O)C4CC4)C1
CACTVS 3.370NC(=N)N1CCC[C@@H](CNC(=O)C[C@H](N[S](=O)(=O)c2ccc3ccccc3c2)C(=O)N(CC(O)=O)C4CC4)C1
OpenEye OEToolkits 1.7.6[H]/N=C(/N)\N1CCC[C@H](C1)CNC(=O)C[C@@H](C(=O)N(CC(=O)O)C2CC2)NS(=O)(=O)c3ccc4ccccc4c3
OpenEye OEToolkits 1.7.6c1ccc2cc(ccc2c1)S(=O)(=O)NC(CC(=O)NCC3CCCN(C3)C(=N)N)C(=O)N(CC(=O)O)C4CC4
ACDLabs 12.01O=C(O)CN(C(=O)C(NS(=O)(=O)c2cc1ccccc1cc2)CC(=O)NCC3CCCN(C(=[N@H])N)C3)C4CC4
FormulaC26 H34 N6 O6 S
Name2-[[(2S)-4-[[(3S)-1-carbamimidoylpiperidin-3-yl]methylamino]-2-(naphthalen-2-ylsulfonylamino)-4-oxidanylidene-butanoyl] -cyclopropyl-amino]ethanoic acid;
NAPSAGATRAN;
Ro-46-6240
ChEMBLCHEMBL325166
DrugBank
ZINC
PDB chain4ax9 Chain H Residue 1246 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ax9 Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		H57 Y60A E97A N98 L99 D189 A190 C191 S195 W215 G216 E217 G219
Binding residue
(residue number reindexed from 1)		H43 Y47 E94 N95 L96 D192 A193 C194 S198 W220 G221 E222 G223
Annotation score1
Binding affinityMOAD: Ki=0.00027uM
PDBbind-CN: -logKd/Ki=9.57,Ki=0.27nM
BindingDB: Ki=0.3nM
Enzymatic activity
Enzyme Commision number 3.4.21.5: thrombin.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0005509 calcium ion binding
Biological Process
GO:0006508 proteolysis
GO:0007596 blood coagulation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4ax9, PDBe:4ax9, PDBj:4ax9
PDBsum4ax9
PubMed7966150
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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