Structure of PDB 4rn6 Chain A Binding Site BS01

Receptor Information
>4rn6 Chain A (length=284) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EADCGLRPLFEKKSLEDKTERELLESYIDGRIVEGSDAEIGMSPWQVMLF
RKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRT
RYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVC
LPDRETAASLLQAGYKGRVTGWGNLKETWTAPSVLQVVNLPIVERPVCKD
STRIRITDNMFCAGYKPDEGKRGDACEGDAGGPFVMKSPFNNRWYQMGIV
SWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE
Ligand information
Ligand ID15U
InChIInChI=1S/C23H36N6O5S/c1-14-8-10-29(18(12-14)22(31)32)21(30)17(6-4-9-26-23(24)25)28-35(33,34)19-7-3-5-16-11-15(2)13-27-20(16)19/h3,5,7,14-15,17-18,27-28H,4,6,8-13H2,1-2H3,(H,31,32)(H4,24,25,26)/t14-,15+,17+,18-/m1/s1
InChIKeyKXNPVXPOPUZYGB-MXSMSXNCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6[H]/N=C(\N)/NCCC[C@@H](C(=O)N1CC[C@H](C[C@@H]1C(=O)O)C)NS(=O)(=O)c2cccc3c2NC[C@H](C3)C
ACDLabs 12.01O=C(N1C(C(=O)O)CC(C)CC1)C(NS(=O)(=O)c3cccc2c3NCC(C)C2)CCCNC(=[N@H])N
OpenEye OEToolkits 1.7.6CC1CCN(C(C1)C(=O)O)C(=O)C(CCCNC(=N)N)NS(=O)(=O)c2cccc3c2NCC(C3)C
CACTVS 3.370C[C@@H]1CCN([C@H](C1)C(O)=O)C(=O)[C@H](CCCNC(N)=N)N[S](=O)(=O)c2cccc3C[C@H](C)CNc23
CACTVS 3.370C[CH]1CCN([CH](C1)C(O)=O)C(=O)[CH](CCCNC(N)=N)N[S](=O)(=O)c2cccc3C[CH](C)CNc23
FormulaC23 H36 N6 O5 S
Name(2R,4R)-4-methyl-1-(N~2~-{[(3S)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}-L-arginyl)piperidine-2-carboxylic acid;
S-argatroban
ChEMBLCHEMBL502016
DrugBank
ZINCZINC000003917722
PDB chain4rn6 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4rn6 Autoactivation of thrombin precursors.
Resolution3.0 Å
Binding residue
(original residue number in PDB)
H57 Y60A W60D W148 W215 G216
Binding residue
(residue number reindexed from 1)
H74 Y78 W81 W179 W252 G253
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.10,Kd=8uM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 E192 G193 D194 A195 G196
Catalytic site (residue number reindexed from 1) H74 D130 E227 G228 D229 A230 G231
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:4rn6, PDBe:4rn6, PDBj:4rn6
PDBsum4rn6
PubMed23467412
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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