Structure of PDB 5k00 Chain A Binding Site BS01

Receptor Information
>5k00 Chain A (length=311) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDYDELLKYYELHETIGTGAKVKLACHILTGEMVAIKIMDKNTLGSDLPR
IKTEIEALKNLRHQHICQLYHVLETANKIFMVLEYCPGGELFDYIISQDR
LSEEETRVVFRQIVSAVAYVHSQGYAHRDLKPENLLFDEYHKLKLIDFGL
CAKPSLAYAAPELIQGKSYLGSEADVWSMGILLYVLMCGFLPFDDDNVMA
LYKKIMRGKYDVPKWLSPSSILLLQQMLQVDPKKRISMKNLLNHPWIMQD
YNYPVEWQSKNPFIHLDDDCVTELSVHHRNNRQTMEDLISLWQYDHLTAT
YLLLLAKKARG
Ligand information
Ligand ID6PV
InChIInChI=1S/C32H34N6O4/c1-41-27-9-5-8-26(18-27)37-32-35-19-28(31(38-32)42-21-22-14-16-33-17-15-22)23-10-12-24(13-11-23)30(40)34-20-29(39)36-25-6-3-2-4-7-25/h2-13,18-19,22,33H,14-17,20-21H2,1H3,(H,34,40)(H,36,39)(H,35,37,38)
InChIKeyAJPBKLULISUYTP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1cccc(Nc2ncc(c3ccc(cc3)C(=O)NCC(=O)Nc4ccccc4)c(OCC5CCNCC5)n2)c1
ACDLabs 12.01c2(ncc(c(OCC1CCNCC1)n2)c4ccc(C(=O)NCC(=O)Nc3ccccc3)cc4)Nc5cccc(OC)c5
OpenEye OEToolkits 2.0.4COc1cccc(c1)Nc2ncc(c(n2)OCC3CCNCC3)c4ccc(cc4)C(=O)NCC(=O)Nc5ccccc5
FormulaC32 H34 N6 O4
Name4-{2-[(3-methoxyphenyl)amino]-4-[(piperidin-4-yl)methoxy]pyrimidin-5-yl}-N-[2-oxo-2-(phenylamino)ethyl]benzamide
ChEMBL
DrugBank
ZINCZINC000584904664
PDB chain5k00 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5k00 Addition" and "Subtraction": Selectivity Design for Type II Maternal Embryonic Leucine Zipper Kinase Inhibitors.
Resolution1.77 Å
Binding residue
(original residue number in PDB)		A38 K40 L61 L64 C70 L86 Y88 C89 G92 E93 L139 I149 D150 F151
Binding residue
(residue number reindexed from 1)		A35 K37 L58 L61 C67 L83 Y85 C86 G89 E90 L136 I146 D147 F148
Annotation score1
Binding affinityMOAD: ic50=7nM
PDBbind-CN: -logKd/Ki=8.15,IC50=7nM
Enzymatic activity
Catalytic site (original residue number in PDB) D132 K134 E136 N137 D150 S171
Catalytic site (residue number reindexed from 1) D129 K131 E133 N134 D147 S155
Enzyme Commision number 2.7.10.2: non-specific protein-tyrosine kinase.
2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:5k00, PDBe:5k00, PDBj:5k00
PDBsum5k00
PubMed28186750
UniProtQ14680|MELK_HUMAN Maternal embryonic leucine zipper kinase (Gene Name=MELK)

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