Structure of PDB 8rdx Chain B Binding Site BS02

Receptor Information
>8rdx Chain B (length=346) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDFLRDRHVRFFQRCLQVLPERYSSLETSRLTIAFFALSGLDMLDSLDVV
NKDDIIEWIYSLQVLPTEDRSNLDRCGFRGSSYLGIPFNPSKNPGTAHPY
DSGHIAMTYTGLSCLIILGDDLSRVDKEACLAGLRALQLEDGSFCAVPEG
SENDMRFVYCASCICYMLNNWSGMDMKKAISYIRRSMSYDNGLAQGAGLE
SHGGSTFCGIASLCLMGKLEEVFSEKELNRIKRWCIMRQQNGYHGRPNKP
VDTCYSFWVGATLKLLKIFQYTNFEKNRNYILSTQDRLVGGFAKWPDSHP
DALHAYFGICGLSLMEESGICKVHPALNVSTRTSERLRDLHQSWKT
Ligand information
Ligand IDA1HZ4
InChIInChI=1S/C26H29F3N2O4/c1-34-21-11-7-6-10-19(21)20-17-30-22(32)16-24(20)12-14-31(15-13-24)23(33)25(35-2,26(27,28)29)18-8-4-3-5-9-18/h3-11,20H,12-17H2,1-2H3,(H,30,32)/t20-,25+/m0/s1
InChIKeyRLJMERPAJNBSDE-NBGIEHNGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccccc1[C@@H]2CNC(=O)CC23CCN(CC3)C(=O)[C@](OC)(c4ccccc4)C(F)(F)F
OpenEye OEToolkits 2.0.7COc1ccccc1C2CNC(=O)CC23CCN(CC3)C(=O)C(c4ccccc4)(C(F)(F)F)OC
CACTVS 3.385COc1ccccc1[CH]2CNC(=O)CC23CCN(CC3)C(=O)[C](OC)(c4ccccc4)C(F)(F)F
OpenEye OEToolkits 2.0.7COc1ccccc1[C@@H]2CNC(=O)CC23CCN(CC3)C(=O)[C@](c4ccccc4)(C(F)(F)F)OC
FormulaC26 H29 F3 N2 O4
Name(5~{R})-5-(2-methoxyphenyl)-9-[(2~{R})-3,3,3-tris(fluoranyl)-2-methoxy-2-phenyl-propanoyl]-3,9-diazaspiro[5.5]undecan-2-one
ChEMBL
DrugBank
ZINC
PDB chain8rdx Chain B Residue 404 [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]
PDB8rdx Novel YAP1/TAZ pathway inhibitors identified through phenotypic screening with potent anti-tumor activity via blockade of GGTase-I / Rho-GTPase signaling
Resolution3.67 Å
Binding residue
(original residue number in PDB)		A123 R173 H219 G221 S222 C225 W275
Binding residue
(residue number reindexed from 1)		A106 R156 H202 G204 S205 C208 W258
Annotation score1
Enzymatic activity
Enzyme Commision number 2.5.1.59: protein geranylgeranyltransferase type I.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004659 prenyltransferase activity
GO:0004661 protein geranylgeranyltransferase activity
GO:0004662 CAAX-protein geranylgeranyltransferase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0008318 protein prenyltransferase activity
GO:0036094 small molecule binding
GO:0042277 peptide binding
GO:0046872 metal ion binding
GO:1901363 heterocyclic compound binding
Biological Process
GO:0008284 positive regulation of cell population proliferation
GO:0018344 protein geranylgeranylation
GO:0034097 response to cytokine
GO:0045787 positive regulation of cell cycle
GO:0051771 negative regulation of nitric-oxide synthase biosynthetic process
Cellular Component
GO:0005953 CAAX-protein geranylgeranyltransferase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8rdx, PDBe:8rdx, PDBj:8rdx
PDBsum8rdx
PubMed38537632
UniProtP53610|PGTB1_RAT Geranylgeranyl transferase type-1 subunit beta (Gene Name=Pggt1b)

[Back to BioLiP]