Structure of PDB 2vdy Chain B Binding Site BS01

Receptor Information
>2vdy Chain B (length=361) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLASANVDFAFSLYKHLVALSPKKNIFISPVSISMALAMLSLGTCGHTRA
QLLQGLGFNLSETEIHQGFQHLHQLFAKSDTSLEMTMGNALFLDGSLELL
ESFSADIKHYYESEVLAMNFQDWATASRQINSYVKNKTQGKIVDLFSSPA
ILVLVNYIFFKGTWTQPFDLASTREENFYVDETTVVKVPMMLQSSTISYL
HDSELPCQLVQMNYVGNGTVFFILPDKGKMNTVIAALSRDTINRWSAGLT
SSQVDLYIPKVTISGVYDLGDVLEEMGIADLFTTQANFSRITQDAQLKSS
KVVHKAVLQLNEEGTEAAGAMFLEAIPRKPIILRFNQPFIIMIFDHFTWS
SLFLARVMNPV
Ligand information
Ligand IDHCY
InChIInChI=1S/C21H30O5/c1-19-7-5-13(23)9-12(19)3-4-14-15-6-8-21(26,17(25)11-22)20(15,2)10-16(24)18(14)19/h9,14-16,18,22,24,26H,3-8,10-11H2,1-2H3/t14-,15-,16-,18+,19-,20-,21-/m0/s1
InChIKeyJYGXADMDTFJGBT-VWUMJDOOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC12CCC(=O)C=C1CCC3C2C(CC4(C3CCC4(C(=O)CO)O)C)O
CACTVS 3.341C[C]12CCC(=O)C=C1CC[CH]3[CH]4CC[C](O)(C(=O)CO)[C]4(C)C[CH](O)[CH]23
CACTVS 3.341C[C@]12CCC(=O)C=C1CC[C@H]3[C@@H]4CC[C@](O)(C(=O)CO)[C@@]4(C)C[C@H](O)[C@H]23
OpenEye OEToolkits 1.5.0C[C@]12CCC(=O)C=C1CC[C@@H]3[C@@H]2[C@H](C[C@]4([C@H]3CC[C@@]4(C(=O)CO)O)C)O
ACDLabs 10.04O=C(CO)C3(O)C2(CC(O)C4C1(C(=CC(=O)CC1)CCC4C2CC3)C)C
FormulaC21 H30 O5
Name(11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione;
CORTISOL
ChEMBLCHEMBL389621
DrugBankDB00741
ZINCZINC000013540519
PDB chain2vdy Chain B Residue 1384 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2vdy The S-to-R Transition of Corticosteroid-Binding Globulin and the Mechanism of Hormone Release.
Resolution2.3 Å
Binding residue
(original residue number in PDB)
S19 V22 R260 N264 F366 H368 W371
Binding residue
(residue number reindexed from 1)
S4 V7 R239 N243 F344 H346 W349
Annotation score1
Binding affinityBindingDB: Ki=13nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004867 serine-type endopeptidase inhibitor activity
GO:0005496 steroid binding
Biological Process
GO:0008211 glucocorticoid metabolic process
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0070062 extracellular exosome

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:2vdy, PDBe:2vdy, PDBj:2vdy
PDBsum2vdy
PubMed18513745
UniProtP08185|CBG_HUMAN Corticosteroid-binding globulin (Gene Name=SERPINA6)

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