Structure of PDB 1nm6 Chain A Binding Site BS02

Receptor Information
>1nm6 Chain A (length=276) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DCGLRPLFEKKSLEDKTERELLESYIIVEGSDAEIGMSPWQVMLFRKSPQ
ELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERN
IEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRE
TAASLLQAGYKGRVTGWGNLKEGQPSVLQVVNLPIVERPVCKDSTRIRIT
DNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCD
RDGKYGFYTHVFRLKKWIQKVIDQFG
Ligand information
Ligand IDL86
InChIInChI=1S/C27H33ClN6O2/c28-24-18-32-26-27(36)34(24)19-25(35)31-16-22-10-5-4-9-21(22)11-14-29-12-6-13-30-17-23(33-26)15-20-7-2-1-3-8-20/h1-5,7-10,18,23,29-30H,6,11-17,19H2,(H,31,35)(H,32,33)/t23-/m0/s1
InChIKeyLYVSCNRRXJZCRV-QHCPKHFHSA-N
SMILES
SoftwareSMILES
CACTVS 3.341ClC1=CN=C2N[CH](CNCCCNCCc3ccccc3CNC(=O)CN1C2=O)Cc4ccccc4
CACTVS 3.341ClC1=CN=C2N[C@H](CNCCCNCCc3ccccc3CNC(=O)CN1C2=O)Cc4ccccc4
OpenEye OEToolkits 1.5.0c1ccc(cc1)C[C@H]2CNCCCNCCc3ccccc3CNC(=O)CN4C(=CN=C(C4=O)N2)Cl
OpenEye OEToolkits 1.5.0c1ccc(cc1)CC2CNCCCNCCc3ccccc3CNC(=O)CN4C(=CN=C(C4=O)N2)Cl
ACDLabs 10.04O=C3NCc1ccccc1CCNCCCNCC(NC2=NC=C(Cl)N(C2=O)C3)Cc4ccccc4
FormulaC27 H33 Cl N6 O2
Name(11S)-11-BENZYL-6-CHLORO-1,2,10,11,12,13,14,15,16,17,18,19-DODECAHYDRO-5,9-METHANO-2,5,8,10,13,17-BENZOHEXAAZACYCLOHENI COSINE-3,24-DIONE;
COMPOUND 31
ChEMBLCHEMBL327421
DrugBank
ZINCZINC000003991144
PDB chain1nm6 Chain A Residue 247 [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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PDB1nm6 Design and synthesis of potent and selective macrocyclic thrombin inhibitors
Resolution1.8 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D E97A N98 L99 A190 S195 V213 S214 W215 G216
Binding residue
(residue number reindexed from 1)		H69 Y73 W76 E120 N121 L122 A218 S223 V243 S244 W245 G246
Annotation score1
Binding affinityMOAD: Ki=0.09nM
PDBbind-CN: -logKd/Ki=10.05,Ki=0.09nM
BindingDB: Ki=0.090000nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 E192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H69 D125 E220 G221 D222 S223 G224
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:1nm6, PDBe:1nm6, PDBj:1nm6
PDBsum1nm6
PubMed12873514
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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