Structure of PDB 6rot Chain H Binding Site BS03

Receptor Information
>6rot Chain H (length=250) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEGQPS
VLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGP
FVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
Ligand information
Ligand IDKDQ
InChIInChI=1S/C22H26ClN3O5S/c23-19-9-8-17(14-27)18(11-19)12-24-22(29)20-7-4-10-26(20)21(28)13-25-32(30,31)15-16-5-2-1-3-6-16/h1-3,5-6,8-9,11,20,25,27H,4,7,10,12-15H2,(H,24,29)/t20-/m0/s1
InChIKeyZWZCPMJCUATTCO-FQEVSTJZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)CS(=O)(=O)NCC(=O)N2CCCC2C(=O)NCc3cc(ccc3CO)Cl
CACTVS 3.385OCc1ccc(Cl)cc1CNC(=O)[C@@H]2CCCN2C(=O)CN[S](=O)(=O)Cc3ccccc3
CACTVS 3.385OCc1ccc(Cl)cc1CNC(=O)[CH]2CCCN2C(=O)CN[S](=O)(=O)Cc3ccccc3
OpenEye OEToolkits 2.0.7c1ccc(cc1)CS(=O)(=O)NCC(=O)N2CCC[C@H]2C(=O)NCc3cc(ccc3CO)Cl
FormulaC22 H26 Cl N3 O5 S
Name(2~{S})-~{N}-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]-1-[2-[(phenylmethyl)sulfonylamino]ethanoyl]pyrrolidine-2-carboxamide
ChEMBLCHEMBL4564064
DrugBank
ZINC
PDB chain6rot Chain H Residue 301 [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]
PDB6rot Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding.
Resolution1.339 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D E97A A190 S195 V213 S214 W215 G216 E217 F227
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 E94 A192 S197 V217 S218 W219 G220 E221 F231
Annotation score1
Binding affinityMOAD: Ki=483.63nM
PDBbind-CN: -logKd/Ki=6.32,Ki=483.63nM
BindingDB: Ki=484nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 E192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H43 D99 E194 G195 D196 S197 G198
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:6rot, PDBe:6rot, PDBj:6rot
PDBsum6rot
PubMed31633354
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

[Back to BioLiP]