Structure of PDB 2ykb Chain A Binding Site BS01

Receptor Information
>2ykb Chain A (length=207) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
METFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTD
PSKLDSGKELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGTIAKSGTK
AFMEALQAGADISMIGQFGVGFYSAYLVAEKVTVITKHNDDEQYAWESSA
GGSFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKHSQFIGY
PITLFVE
Ligand information
Ligand IDYKB
InChIInChI=1S/C23H19N5O2/c24-19(29)8-9-20(30)28-22-14-5-2-1-4-13(14)21-15(22)6-3-7-16(21)23-26-17-10-11-25-12-18(17)27-23/h1-7,10-12,22H,8-9H2,(H2,24,29)(H,26,27)(H,28,30)/t22-/m1/s1
InChIKeyROTVJYWUPWSGIX-JOCHJYFZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2c1ccc2c(c1)-c3c(cccc3[C@@H]2NC(=O)CCC(=O)N)c4[nH]c5cnccc5n4
OpenEye OEToolkits 1.7.2c1ccc2c(c1)-c3c(cccc3C2NC(=O)CCC(=O)N)c4[nH]c5cnccc5n4
CACTVS 3.370NC(=O)CCC(=O)N[CH]1c2ccccc2c3c1cccc3c4[nH]c5cnccc5n4
CACTVS 3.370NC(=O)CCC(=O)N[C@@H]1c2ccccc2c3c1cccc3c4[nH]c5cnccc5n4
ACDLabs 12.01O=C(N)CCC(=O)NC5c1ccccc1c4c5cccc4c3nc2ccncc2n3
FormulaC23 H19 N5 O2
NameN-[4-(3H-IMIDAZO[4,5-C]PYRIDIN-2-YL)-9H-FLUOREN-9-YL]-SUCCINAMIDE
ChEMBL
DrugBank
ZINCZINC000073196874
PDB chain2ykb Chain A Residue 1224 [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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PDB2ykb Tricyclic Series of Heat Shock Protein 90 (Hsp90) Inhibitors Part I: Discovery of Tricyclic Imidazo[4,5-C]Pyridines as Potent Inhibitors of the Hsp90 Molecular Chaperone.
Resolution1.93 Å
Binding residue
(original residue number in PDB)		F22 I26 A55 M98 L103 I104 L107 G108 F138 Y139 W162 F170
Binding residue
(residue number reindexed from 1)		F6 I10 A39 M82 L87 I88 L91 G92 F122 Y123 W146 F154
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.96,IC50=1.1uM
Enzymatic activity
Enzyme Commision number 3.6.4.10: non-chaperonin molecular chaperone ATPase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
GO:0051082 unfolded protein binding
GO:0140662 ATP-dependent protein folding chaperone
Biological Process
GO:0006457 protein folding

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2ykb, PDBe:2ykb, PDBj:2ykb
PDBsum2ykb
PubMed21972823
UniProtP07900|HS90A_HUMAN Heat shock protein HSP 90-alpha (Gene Name=HSP90AA1)

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