Structure of PDB 1k21 Chain H Binding Site BS05

Receptor Information
>1k21 Chain H (length=249) 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
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQ
Ligand information
Ligand IDIGN
InChIInChI=1S/C21H38N6O4/c22-21(23)25-11-6-10-24-19(30)17-9-4-5-12-27(17)20(31)16(26-14-18(28)29)13-15-7-2-1-3-8-15/h15-17,26H,1-14H2,(H,24,30)(H,28,29)(H4,22,23,25)/t16-,17+/m1/s1
InChIKeyCDPROXZBMHOBTQ-SJORKVTESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1CCC(CC1)CC(C(=O)N2CCCCC2C(=O)NCCCNC(=N)N)NCC(=O)O
ACDLabs 10.04O=C(N1C(C(=O)NCCCNC(=[N@H])N)CCCC1)C(NCC(=O)O)CC2CCCCC2
CACTVS 3.341NC(=N)NCCCNC(=O)[CH]1CCCCN1C(=O)[CH](CC2CCCCC2)NCC(O)=O
OpenEye OEToolkits 1.5.0C1CCC(CC1)C[C@H](C(=O)N2CCCC[C@H]2C(=O)NCCCNC(=N)N)NCC(=O)O
CACTVS 3.341NC(=N)NCCCNC(=O)[C@@H]1CCCCN1C(=O)[C@@H](CC2CCCCC2)NCC(O)=O
FormulaC21 H38 N6 O4
Name{[(1R)-2-((2S)-2-{[(3-{[AMINO(IMINO)METHYL]AMINO}PROPYL)AMINO]CARBONYL}PIPERIDINYL)-1-(CYCLOHEXYLMETHYL)-2-OXOETHYL]AMINO}ACETIC ACID;
INOGATRAN (ASTRA-ZENECA)
ChEMBLCHEMBL114715
DrugBank
ZINCZINC000003794149
PDB chain1k21 Chain H Residue 999 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1k21 Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition.
Resolution1.86 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D D189 A190 C191 S195 S214 W215 G216 E217 G219
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 D192 A193 C194 S198 S219 W220 G221 E222 G223
Annotation score1
Binding affinityMOAD: Ki=4.2nM
PDBbind-CN: -logKd/Ki=8.38,Ki=4.2nM
BindingDB: Ki=15nM,IC50=1300nM
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:1k21, PDBe:1k21, PDBj:1k21
PDBsum1k21
PubMed11676542
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

[Back to BioLiP]