Structure of PDB 1d9i Chain A Binding Site BS02

Receptor Information
>1d9i Chain A (length=279) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADCGLRPLFEKKSLEDKTERELLESYIDIVEGSDAEIGMSPWQVMLFRKS
PQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYE
RNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPD
RETAASLLQAGYKGRVTGWGNLKETGQPSVLQVVNLPIVERPVCKDSTRI
RITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGE
GCDRDGKYGFYTHVFRLKKWIQKVIDQFG
Ligand information
Ligand ID00P
InChIInChI=1S/C22H29N5O5S/c23-17-10-8-16(9-11-17)15-24-20(28)19-7-4-12-26-21(29)25(22(30)27(19)26)13-14-33(31,32)18-5-2-1-3-6-18/h1-7,16-17,19H,8-15,23H2,(H,24,28)/t16-,17-,19-/m0/s1
InChIKeyPTMIAKQUJFKTNB-LNLFQRSKSA-N
SMILES
SoftwareSMILES
CACTVS 3.370N[CH]1CC[CH](CC1)CNC(=O)[CH]2C=CCN3N2C(=O)N(CC[S](=O)(=O)c4ccccc4)C3=O
ACDLabs 12.01O=S(=O)(c1ccccc1)CCN2C(=O)N3N(C2=O)C(C=CC3)C(=O)NCC4CCC(N)CC4
CACTVS 3.370N[C@@H]1CC[C@H](CC1)CNC(=O)[C@@H]2C=CCN3N2C(=O)N(CC[S](=O)(=O)c4ccccc4)C3=O
OpenEye OEToolkits 1.7.0c1ccc(cc1)S(=O)(=O)CCN2C(=O)N3CC=CC(N3C2=O)C(=O)NCC4CCC(CC4)N
OpenEye OEToolkits 1.7.0c1ccc(cc1)S(=O)(=O)CCN2C(=O)N3CC=C[C@H](N3C2=O)C(=O)NCC4CCC(CC4)N
FormulaC22 H29 N5 O5 S
Name(5S)-N-[(trans-4-aminocyclohexyl)methyl]-1,3-dioxo-2-[2-(phenylsulfonyl)ethyl]-2,3,5,8-tetrahydro-1H-[1,2,4]triazolo[1,2-a]pyridazine-5-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain1d9i Chain A Residue 380 [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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PDB1d9i Structure of thrombin complexed with selective non-electrophilic inhibitors having cyclohexyl moieties at P1.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D I174 C191 E192 S214 W215 G216 E217 G219
Binding residue
(residue number reindexed from 1)		H71 Y75 W78 I200 C222 E223 S247 W248 G249 E250 G251
Annotation score1
Binding affinityMOAD: Ki=0.78nM
PDBbind-CN: -logKd/Ki=9.11,Ki=0.78nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 E192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H71 D127 E223 G224 D225 S226 G227
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
Cellular Component
GO:0005576 extracellular region

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1d9i, PDBe:1d9i, PDBj:1d9i
PDBsum1d9i
PubMed10713516
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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