Structure of PDB 5gjd Chain A Binding Site BS01

Receptor Information
>5gjd Chain A (length=292) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPLHMIDYKEIEVEEVVGRGAFGVVCKAKWRAKDVAIKQIESESERKAFI
VELRQLSRVNHPNIVKLYGACLNPVCLVMEYAEGGSLYNVLHGAEPLPYY
TAAHAMSWCLQCSQGVAYLHSMQPKALIHRDLKPPNLLLVAGGTVLKICD
FGTACGSAAWMAPEVFEGSNYSEKCDVFSWGIILWEVITRRKPFDEIGGP
AFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKIMT
HLMRYFPGADEPLQYPCQHSLPGRVEPYVDFAEFYRLWSVDH
Ligand information
Ligand ID6V3
InChIInChI=1S/C29H28N6O2/c1-34-15-17-35(18-16-34)26-4-2-3-20-19-22(7-10-24(20)26)33-29(36)32-21-5-8-23(9-6-21)37-27-12-14-31-28-25(27)11-13-30-28/h2-14,19H,15-18H2,1H3,(H,30,31)(H2,32,33,36)
InChIKeyWQRGBJPKMNUGRL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5CN1CCN(CC1)c2cccc3c2ccc(c3)NC(=O)Nc4ccc(cc4)Oc5ccnc6c5cc[nH]6
CACTVS 3.385CN1CCN(CC1)c2cccc3cc(NC(=O)Nc4ccc(Oc5ccnc6[nH]ccc56)cc4)ccc23
FormulaC29 H28 N6 O2
Name1-(4-((1H-pyrrolo[2,3-b]pyridin-4-yl)oxy)phenyl)-3-(5-(4-methylpiperazin-1-yl)naphthalen-2-yl)urea
ChEMBLCHEMBL4095421
DrugBank
ZINCZINC000584905231
PDB chain5gjd Chain A Residue 601 [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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PDB5gjd Development of a Method for Converting a TAK1 Type I Inhibitor into a Type II or c-Helix-Out Inhibitor by Structure-Based Drug Design (SBDD)
Resolution2.79 Å
Binding residue
(original residue number in PDB)		V50 A61 E77 Q80 L81 M104 Y106 A107 I153 H154 L163 C174 D175 F176
Binding residue
(residue number reindexed from 1)		V25 A36 E52 Q55 L56 M79 Y81 A82 I128 H129 L138 C149 D150 F151
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.92,Kd=12nM
Enzymatic activity
Catalytic site (original residue number in PDB) D156 K158 P160 N161 I173 D175
Catalytic site (residue number reindexed from 1) D131 K133 P135 N136 I148 D150
Enzyme Commision number 2.7.11.25: mitogen-activated protein kinase kinase kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004672 protein kinase activity
GO:0004709 MAP kinase kinase kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation
GO:0007165 signal transduction

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:5gjd, PDBe:5gjd, PDBj:5gjd
PDBsum5gjd
PubMed27803473
UniProtO43318|M3K7_HUMAN Mitogen-activated protein kinase kinase kinase 7 (Gene Name=MAP3K7);
Q15750|TAB1_HUMAN TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 (Gene Name=TAB1)

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