Structure of PDB 9ax6 Chain D Binding Site BS01

Receptor Information
>9ax6 Chain D (length=164) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGS
CFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMA
NAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGK
TSKKITIADCGQLE
Ligand information
Ligand IDA1AHB
InChIInChI=1S/C44H58N8O5S/c1-8-51-37-12-11-28-19-31(37)33(40(51)32-20-29(23-45-39(32)27(3)56-7)50-16-14-49(6)15-17-50)22-44(4,5)25-57-43(55)34-10-9-13-52(48-34)42(54)35(21-38-46-36(28)24-58-38)47-41(53)30-18-26(30)2/h11-12,19-20,23-24,26-27,30,34-35,48H,8-10,13-18,21-22,25H2,1-7H3,(H,47,53)/t26-,27+,30+,34+,35-/m0/s1
InChIKeyFVICRBSEYSHKFY-MYQJQZSQSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCn1c2ccc3cc2c(CC(C)(C)COC(=O)[C@@H]4CCC[N@](N4)C(=O)[C@H](Cc5scc3n5)NC(=O)[C@H]6C[C@@H]6C)c1c7cc(cnc7[C@H](C)OC)N8CCN(C)CC8
OpenEye OEToolkits 2.0.7CCn1c2ccc-3cc2c(c1c4cc(cnc4[C@H](C)OC)N5CCN(CC5)C)CC(COC(=O)[C@@H]6CCCN(N6)C(=O)[C@H](Cc7nc3cs7)NC(=O)[C@H]8C[C@@H]8C)(C)C
CACTVS 3.385CCn1c2ccc3cc2c(CC(C)(C)COC(=O)[CH]4CCC[N](N4)C(=O)[CH](Cc5scc3n5)NC(=O)[CH]6C[CH]6C)c1c7cc(cnc7[CH](C)OC)N8CCN(C)CC8
OpenEye OEToolkits 2.0.7CCn1c2ccc-3cc2c(c1c4cc(cnc4C(C)OC)N5CCN(CC5)C)CC(COC(=O)C6CCCN(N6)C(=O)C(Cc7nc3cs7)NC(=O)C8CC8C)(C)C
ACDLabs 12.01CN1CCN(CC1)c1cc(c(nc1)C(C)OC)c1n(CC)c2ccc3cc2c1CC(C)(C)COC(=O)C1CCCN(N1)C(=O)C(Cc1nc3cs1)NC(=O)C1CC1C
FormulaC44 H58 N8 O5 S
Name(1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain9ax6 Chain D Residue 201 [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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PDB9ax6 Translational and Therapeutic Evaluation of RAS-GTP Inhibition by RMC-6236 in RAS-Driven Cancers.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		R55 F60 M61 Q63 A101 N102 Q111 F113 W121 H126 R148
Binding residue
(residue number reindexed from 1)		R54 F59 M60 Q62 A100 N101 Q110 F112 W120 H125 R147
Annotation score1
Enzymatic activity
Enzyme Commision number 5.2.1.8: peptidylprolyl isomerase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003755 peptidyl-prolyl cis-trans isomerase activity
GO:0005178 integrin binding
GO:0005515 protein binding
GO:0016018 cyclosporin A binding
GO:0046790 virion binding
GO:0051082 unfolded protein binding
GO:1904399 heparan sulfate binding
Biological Process
GO:0000413 protein peptidyl-prolyl isomerization
GO:0001933 negative regulation of protein phosphorylation
GO:0001934 positive regulation of protein phosphorylation
GO:0006457 protein folding
GO:0006469 negative regulation of protein kinase activity
GO:0006915 apoptotic process
GO:0019076 viral release from host cell
GO:0030168 platelet activation
GO:0030182 neuron differentiation
GO:0030593 neutrophil chemotaxis
GO:0030595 leukocyte chemotaxis
GO:0032148 activation of protein kinase B activity
GO:0032873 negative regulation of stress-activated MAPK cascade
GO:0034389 lipid droplet organization
GO:0034599 cellular response to oxidative stress
GO:0042118 endothelial cell activation
GO:0043410 positive regulation of MAPK cascade
GO:0045069 regulation of viral genome replication
GO:0045070 positive regulation of viral genome replication
GO:0050714 positive regulation of protein secretion
GO:0051092 positive regulation of NF-kappaB transcription factor activity
GO:0060352 cell adhesion molecule production
GO:0061944 negative regulation of protein K48-linked ubiquitination
GO:0070527 platelet aggregation
GO:1902176 negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
GO:1903901 negative regulation of viral life cycle
GO:2001233 regulation of apoptotic signaling pathway
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0031982 vesicle
GO:0032991 protein-containing complex
GO:0034774 secretory granule lumen
GO:0070062 extracellular exosome
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:9ax6, PDBe:9ax6, PDBj:9ax6
PDBsum9ax6
PubMed38593348
UniProtP62937|PPIA_HUMAN Peptidyl-prolyl cis-trans isomerase A (Gene Name=PPIA)

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