Structure of PDB 1nt1 Chain A Binding Site BS02

Receptor Information
>1nt1 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 IDT76
InChIInChI=1S/C25H33ClN4O5/c26-18-8-9-20-17(13-18)14-28-24(33)19-7-4-12-30(19)25(34)23(16-5-2-1-3-6-16)29-21(31)10-11-27-22(32)15-35-20/h8-9,13,16,19,23H,1-7,10-12,14-15H2,(H,27,32)(H,28,33)(H,29,31)/t19-,23+/m0/s1
InChIKeyCNGULIMOMYJRBP-WMZHIEFXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc2c(cc1Cl)CNC(=O)C3CCCN3C(=O)C(NC(=O)CCNC(=O)CO2)C4CCCCC4
CACTVS 3.341Clc1ccc2OCC(=O)NCCC(=O)N[CH](C3CCCCC3)C(=O)N4CCC[CH]4C(=O)NCc2c1
CACTVS 3.341Clc1ccc2OCC(=O)NCCC(=O)N[C@H](C3CCCCC3)C(=O)N4CCC[C@H]4C(=O)NCc2c1
OpenEye OEToolkits 1.5.0c1cc2c(cc1Cl)CNC(=O)[C@@H]3CCCN3C(=O)[C@H](NC(=O)CCNC(=O)CO2)C4CCCCC4
ACDLabs 10.04Clc4cc1c(OCC(=O)NCCC(=O)NC(C(=O)N2C(C(=O)NC1)CCC2)C3CCCCC3)cc4
FormulaC25 H33 Cl N4 O5
Name(6R,21AS)-17-CHLORO-6-CYCLOHEXYL-2,3,6,7,10,11,19,20-OCTAHYDRO-1H,5H-PYRROLO[1,2-K][1,4,8,11,14]BENZOXATETRAAZA-CYCLOHEPTADECINE-5,8,12,21(9H,13H,21AH)-TETRONE
ChEMBLCHEMBL1236167
DrugBank
ZINCZINC000013537324
PDB chain1nt1 Chain A Residue 247 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1nt1 Design and synthesis of potent and selective macrocyclic thrombin inhibitors
Resolution2.0 Å
Binding residue
(original residue number in PDB)		H57 Y60A S195 V213 S214 W215 G216 G219 F227
Binding residue
(residue number reindexed from 1)		H69 Y73 S223 V243 S244 W245 G246 G248 F257
Annotation score1
Binding affinityMOAD: Ki=1.3nM
PDBbind-CN: -logKd/Ki=8.89,Ki=1.3nM
BindingDB: Ki=1.3nM
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:1nt1, PDBe:1nt1, PDBj:1nt1
PDBsum1nt1
PubMed12873514
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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