Structure of PDB 2cf9 Chain H Binding Site BS03

Receptor Information
>2cf9 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 ID348
InChIInChI=1S/C27H34N4O2/c1-16(2)24-22-21-5-4-14-30(21)25(18-8-10-19(11-9-18)26(28)29)23(22)27(32)31(24)15-17-6-12-20(33-3)13-7-17/h6-13,16,21-25H,4-5,14-15H2,1-3H3,(H3,28,29)/t21-,22-,23-,24+,25-/m0/s1
InChIKeyXETNTDPUFDNJKX-BDUWWWMKSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C3N(C(C4C1N(CCC1)C(c2ccc(C(=[N@H])N)cc2)C34)C(C)C)Cc5ccc(OC)cc5
CACTVS 3.341COc1ccc(CN2[CH](C(C)C)[CH]3[CH]4CCCN4[CH]([CH]3C2=O)c5ccc(cc5)C(N)=N)cc1
CACTVS 3.341COc1ccc(CN2[C@H](C(C)C)[C@H]3[C@@H]4CCCN4[C@H]([C@H]3C2=O)c5ccc(cc5)C(N)=N)cc1
OpenEye OEToolkits 1.5.0[H]N=C(c1ccc(cc1)C2C3C(C4N2CCC4)C(N(C3=O)Cc5ccc(cc5)OC)C(C)C)N
OpenEye OEToolkits 1.5.0[H]/N=C(\c1ccc(cc1)[C@H]2[C@@H]3[C@H]([C@H]4[N@@]2CCC4)[C@H](N(C3=O)Cc5ccc(cc5)OC)C(C)C)/N
FormulaC27 H34 N4 O2
Name4-[(1R,3AS,4R,8AS,8BR)-1-ISOPROPYL-2-(4-METHOXYBENZYL)-3-OXODECAHYDROPYRROLO[3,4-A]PYRROLIZIN-4-YL]BENZENECARBOXIMIDAMIDE
ChEMBLCHEMBL1230037
DrugBank
ZINCZINC000016051886
PDB chain2cf9 Chain H Residue 1247 [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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PDB2cf9 Multipolar Interactions in the D Pocket of Thrombin: Large Differences between Tricyclic Imide and Lactam Inhibitors.
Resolution1.79 Å
Binding residue
(original residue number in PDB)		H57 Y60A N98 D189 A190 S214 W215 G216 G219
Binding residue
(residue number reindexed from 1)		H43 Y47 N95 D192 A193 S219 W220 G221 G223
Annotation score1
Binding affinityMOAD: Ki=0.015uM
PDBbind-CN: -logKd/Ki=7.82,Ki=0.015uM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:2cf9, PDBe:2cf9, PDBj:2cf9
PDBsum2cf9
PubMed16763681
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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