Structure of PDB 3rkz Chain A Binding Site BS01

Receptor Information
>3rkz Chain A (length=208) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTD
PSKLDSGKELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGTIAKSGTK
AFMEALQAGADISMIGQFGVGFYSAYLVAEKVTVITKHNDDEQYAWESSA
GGSFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKHSQFIGY
PITLFVEK
Ligand information
Ligand ID06T
InChIInChI=1S/C28H39N5O3/c1-15-14-32(27(36)17(3)29)10-9-22-16(2)25-23(12-28(5,6)13-24(25)34)33(22)19-7-8-20(26(30)35)21(11-19)31-18(15)4/h7-8,11,15,17-18,31H,9-10,12-14,29H2,1-6H3,(H2,30,35)/t15-,17+,18+/m1/s1
InChIKeyJSSUIPOIXFFFQU-NJAFHUGGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2Cc1c2n(c3c1C(=O)CC(C3)(C)C)-c4ccc(c(c4)N[C@H]([C@@H](CN(CC2)C(=O)[C@H](C)N)C)C)C(=O)N
CACTVS 3.370C[C@H](N)C(=O)N1CCc2n(c3CC(C)(C)CC(=O)c3c2C)c4ccc(C(N)=O)c(N[C@@H](C)[C@H](C)C1)c4
ACDLabs 12.01O=C2c1c(c3n(c1CC(C)(C)C2)c4ccc(c(NC(C(C)CN(C(=O)C(N)C)CC3)C)c4)C(=O)N)C
OpenEye OEToolkits 1.7.2Cc1c2n(c3c1C(=O)CC(C3)(C)C)-c4ccc(c(c4)NC(C(CN(CC2)C(=O)C(C)N)C)C)C(=O)N
CACTVS 3.370C[CH](N)C(=O)N1CCc2n(c3CC(C)(C)CC(=O)c3c2C)c4ccc(C(N)=O)c(N[CH](C)[CH](C)C1)c4
FormulaC28 H39 N5 O3
Name(5R,6S)-3-(L-alanyl)-5,6,15,15,18-pentamethyl-17-oxo-2,3,4,5,6,7,14,15,16,17-decahydro-1H-12,8-(metheno)[1,5,9]triazacyclotetradecino[1,2-a]indole-9-carboxamide
ChEMBLCHEMBL1807804
DrugBank
ZINCZINC000072177167
PDB chain3rkz Chain A Residue 1 [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]
PDB3rkz Discovery of a stable macrocyclic o-aminobenzamide Hsp90 inhibitor which significantly decreases tumor volume in a mouse xenograft model.
Resolution1.5693 Å
Binding residue
(original residue number in PDB)		N51 M98 L107 F138 Y139 W162 T184
Binding residue
(residue number reindexed from 1)		N35 M82 L91 F122 Y123 W146 T168
Annotation score1
Binding affinityMOAD: ic50=0.083uM
PDBbind-CN: -logKd/Ki=7.08,IC50=83nM
BindingDB: IC50=83nM
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:3rkz, PDBe:3rkz, PDBj:3rkz
PDBsum3rkz
PubMed21715165
UniProtP07900|HS90A_HUMAN Heat shock protein HSP 90-alpha (Gene Name=HSP90AA1)

[Back to BioLiP]