Structure of PDB 4d2t Chain A Binding Site BS01

Receptor Information
>4d2t Chain A (length=316) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKDYDELLKYYELHETIGTGGFAKVKLACHILTGEMVAIKIMDKNTDLPR
IKTEIEALKNLRHQHICQLYHVLETANKIFMVLEYCPGGELFDYIISQDR
LSEEETRVVFRQIVSAVAYVHSQGYAHRDLKPENLLFDEYHKLKLIDFGL
CACCGALAYAAPELIQGKSGSEADVWSMGILLYVLMCGFLPFDDDTAAAL
VAKIMRGKYDVPKWLSPSSILLLQQMLQVDPKKRISMKNLLNHPWIMQDY
NYPVEWQSKNPFIHLDDDCVTELSVHHRNNRQTMEDLISLWQYDHLTATY
LLLLAKKARGKPVRLR
Ligand information
Ligand ID3I7
InChIInChI=1S/C19H20N4O2/c20-9-4-10-25-18-11-14(15-12-21-22-13-15)7-8-17(18)19(24)23-16-5-2-1-3-6-16/h1-3,5-8,11-13H,4,9-10,20H2,(H,21,22)(H,23,24)/p+1
InChIKeyKLMWPYHIMXLJIE-UHFFFAOYSA-O
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(c2c(OCCC[NH3+])cc(c1cnnc1)cc2)Nc3ccccc3
CACTVS 3.385[NH3+]CCCOc1cc(ccc1C(=O)Nc2ccccc2)c3c[nH]nc3
OpenEye OEToolkits 1.7.6c1ccc(cc1)NC(=O)c2ccc(cc2OCCC[NH3+])c3c[nH]nc3
FormulaC19 H21 N4 O2
Name3-[2-(phenylcarbamoyl)-5-(1H-pyrazol-4-yl)phenoxy]propan-1-aminium
ChEMBL
DrugBank
ZINC
PDB chain4d2t Chain A Residue 1334 [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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PDB4d2t Fragment-Based Discovery of Type I Inhibitors of Maternal Embryonic Leucine Zipper Kinase
Resolution2.7 Å
Binding residue
(original residue number in PDB)		A38 K40 E57 C70 E87 Y88 C89 P90 I149
Binding residue
(residue number reindexed from 1)		A38 K40 E54 C67 E84 Y85 C86 P87 I146
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.00,IC50=1.0uM
Enzymatic activity
Catalytic site (original residue number in PDB) D132 K134 E136 N137 D150 A171
Catalytic site (residue number reindexed from 1) D129 K131 E133 N134 D147 A156
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
View graph for
Biological Process
External links
PDB RCSB:4d2t, PDBe:4d2t, PDBj:4d2t
PDBsum4d2t
PubMed25589925
UniProtQ14680|MELK_HUMAN Maternal embryonic leucine zipper kinase (Gene Name=MELK)

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