Structure of PDB 5vgy Chain A Binding Site BS02

Receptor Information
>5vgy Chain A (length=258) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYD
QATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDG
QGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSA
KPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPL
LECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKN
RQIKASFK
Ligand information
Ligand ID9AA
InChIInChI=1S/C12H14N2O4S/c1-17-8-4-3-7(9(5-8)18-2)6-12(16)10(15)13-11(19)14-12/h3-5,16H,6H2,1-2H3,(H2,13,14,15,19)/t12-/m0/s1
InChIKeyHCADMEQVRWTPEA-LBPRGKRZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6COc1ccc(c(c1)OC)CC2(C(=O)NC(=S)N2)O
CACTVS 3.385COc1ccc(C[C]2(O)NC(=S)NC2=O)c(OC)c1
CACTVS 3.385COc1ccc(C[C@@]2(O)NC(=S)NC2=O)c(OC)c1
OpenEye OEToolkits 2.0.6COc1ccc(c(c1)OC)C[C@@]2(C(=O)NC(=S)N2)O
ACDLabs 12.01c1cc(cc(c1CC2(C(NC(=S)N2)=O)O)OC)OC
FormulaC12 H14 N2 O4 S
Name(5S)-5-[(2,4-dimethoxyphenyl)methyl]-5-hydroxy-2-sulfanylideneimidazolidin-4-one
ChEMBLCHEMBL4061548
DrugBank
ZINC
PDB chain5vgy Chain A Residue 304 [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]
PDB5vgy Identification of a New Zinc Binding Chemotype by Fragment Screening.
Resolution1.39 Å
Binding residue
(original residue number in PDB)		H94 H96 H119 V121 F131 V143 L198 T199 T200 W209
Binding residue
(residue number reindexed from 1)		H92 H94 H117 V119 F128 V140 L195 T196 T197 W206
Annotation score1
Binding affinityMOAD: Kd=65.5uM
PDBbind-CN: -logKd/Ki=4.18,Kd=65.5uM
BindingDB: Kd=43600nM
Enzymatic activity
Catalytic site (original residue number in PDB) H64 H94 H96 E106 H119 T199
Catalytic site (residue number reindexed from 1) H62 H92 H94 E104 H117 T196
Enzyme Commision number 4.2.1.1: carbonic anhydrase.
4.2.1.69: cyanamide hydratase.
Gene Ontology
Molecular Function
GO:0004064 arylesterase activity
GO:0004089 carbonate dehydratase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016829 lyase activity
GO:0018820 cyanamide hydratase activity
GO:0046872 metal ion binding
Biological Process
GO:0002009 morphogenesis of an epithelium
GO:0006730 one-carbon metabolic process
GO:0015670 carbon dioxide transport
GO:0032230 positive regulation of synaptic transmission, GABAergic
GO:0032849 positive regulation of cellular pH reduction
GO:0038166 angiotensin-activated signaling pathway
GO:0044070 regulation of monoatomic anion transport
GO:0046903 secretion
GO:0051453 regulation of intracellular pH
GO:0070050 neuron cellular homeostasis
GO:2001150 positive regulation of dipeptide transmembrane transport
GO:2001225 regulation of chloride transport
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0043209 myelin sheath
GO:0045177 apical part of cell
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5vgy, PDBe:5vgy, PDBj:5vgy
PDBsum5vgy
PubMed28817930
UniProtP00918|CAH2_HUMAN Carbonic anhydrase 2 (Gene Name=CA2)

[Back to BioLiP]