Structure of PDB 4yz9 Chain A Binding Site BS01

Receptor Information
>4yz9 Chain A (length=381) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVVIVGKISFCPKDVLGHGAEGTIVYRGMFDNRDVAVKRILPECFSFADR
EVQLLRESDEHPNVIRYFCTEKDRQFQYIAIELCAATLQEYVEQKDFAHL
GLEPITLLQQTTSGLAHLHSLNIVHRDLKPHNILISMPNAHGKIKAMISD
FGLCGTEGWIAPEMLENPTYTVDIFSAGCVFYYVISEGSHPFGKSLQRQA
NILLGACSLDCLHPEKHEDVIARELIEKMIAMDPQKRPSAKHVLKHPFFW
SLEKQLQFFQDVSDRIEKESLDGPIVKQLERGGRAVVKMDWRENITVPLQ
TDLRKFRTYKGGSVRDLLRAMRNKKHHYRELPAEVRETLGSLPDDFVCYF
TSRFPHLLAHTYRAMELCSHERLFQPYYFHE
Ligand information
Ligand ID4K7
InChIInChI=1S/C24H29Cl2N3O/c1-18-3-5-19(6-4-18)14-27-23(30)29-11-2-9-24(17-29)10-12-28(16-24)15-20-7-8-21(25)22(26)13-20/h3-8,13H,2,9-12,14-17H2,1H3,(H,27,30)/t24-/m1/s1
InChIKeyYFDASBFQKMHSSJ-XMMPIXPASA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ccc(CNC(=O)N2CCC[C]3(CCN(Cc4ccc(Cl)c(Cl)c4)C3)C2)cc1
OpenEye OEToolkits 1.9.2Cc1ccc(cc1)CNC(=O)N2CCCC3(C2)CCN(C3)Cc4ccc(c(c4)Cl)Cl
ACDLabs 12.01c1cc(ccc1C)CNC(=O)N4CCCC2(CCN(C2)Cc3ccc(c(c3)Cl)Cl)C4
CACTVS 3.385Cc1ccc(CNC(=O)N2CCC[C@]3(CCN(Cc4ccc(Cl)c(Cl)c4)C3)C2)cc1
OpenEye OEToolkits 1.9.2Cc1ccc(cc1)CNC(=O)N2CCC[C@@]3(C2)CCN(C3)Cc4ccc(c(c4)Cl)Cl
FormulaC24 H29 Cl2 N3 O
Name(5R)-2-(3,4-dichlorobenzyl)-N-(4-methylbenzyl)-2,7-diazaspiro[4.5]decane-7-carboxamide
ChEMBL
DrugBank
ZINCZINC000210920309
PDB chain4yz9 Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4yz9 Long-Range Inhibitor-Induced Conformational Regulation of Human IRE1 alpha Endoribonuclease Activity.
Resolution2.463 Å
Binding residue
(original residue number in PDB)		A581 K599 C605 A609 E612 V613 I626 L679 H686 D711
Binding residue
(residue number reindexed from 1)		A20 K38 C44 A48 E51 V52 I65 L118 H125 D150
Annotation score1
Binding affinityMOAD: Ki=200nM
PDBbind-CN: -logKd/Ki=7.70,IC50=20nM
Enzymatic activity
Catalytic site (original residue number in PDB) D688 K690 N693 D711 T734
Catalytic site (residue number reindexed from 1) D127 K129 N132 D150 T156
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
3.1.26.-
Gene Ontology
Molecular Function
GO:0004521 RNA endonuclease activity
GO:0004540 RNA nuclease activity
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006397 mRNA processing
GO:0006468 protein phosphorylation
GO:0030968 endoplasmic reticulum unfolded protein response

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4yz9, PDBe:4yz9, PDBj:4yz9
PDBsum4yz9
PubMed26438213
UniProtO75460|ERN1_HUMAN Serine/threonine-protein kinase/endoribonuclease IRE1 (Gene Name=ERN1)

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