Structure of PDB 5dry Chain A Binding Site BS01

Receptor Information
>5dry Chain A (length=319) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLA
MENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTNTRPSTGLLRHI
LQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFV
DLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYG
KKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANM
KEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKSWTGKPVSYY
LHTIDRTILENYFSSLKNP
Ligand information
Ligand ID5EK
InChIInChI=1S/C24H18Cl2N8O2/c25-18-6-2-1-5-17(18)23-29-31-32-34(23)14-22(35)28-30-24(36)27-16-10-9-15-11-12-33(21(15)13-16)20-8-4-3-7-19(20)26/h1-13H,14H2,(H,28,35)(H2,27,30,36)
InChIKeyWJGUKFYAVSWTRD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C(=O)(Cn2nnnc2c1ccccc1Cl)NNC(=O)Nc3cc4c(cc3)ccn4c5ccccc5Cl
OpenEye OEToolkits 1.9.2c1ccc(c(c1)c2nnnn2CC(=O)NNC(=O)Nc3ccc4ccn(c4c3)c5ccccc5Cl)Cl
CACTVS 3.385Clc1ccccc1n2ccc3ccc(NC(=O)NNC(=O)Cn4nnnc4c5ccccc5Cl)cc23
FormulaC24 H18 Cl2 N8 O2
NameN-[1-(2-chlorophenyl)-1H-indol-6-yl]-2-{[5-(2-chlorophenyl)-1H-tetrazol-1-yl]acetyl}hydrazinecarboxamide
ChEMBLCHEMBL4586619
DrugBank
ZINCZINC000584904985
PDB chain5dry Chain A Residue 402 [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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PDB5dry Discovery of Novel Dot1L Inhibitors through a Structure-Based Fragmentation Approach.
Resolution2.41 Å
Binding residue
(original residue number in PDB)		F131 P133 Y136 S140 L143 M147 D161 G163 S164 Q168 V169 V240 N241 S268 S269
Binding residue
(residue number reindexed from 1)		F121 P123 Y126 S130 L133 M137 D151 G153 S154 Q158 V159 V230 N231 S258 S259
Annotation score1
Binding affinityMOAD: ic50=20nM
PDBbind-CN: -logKd/Ki=7.70,IC50=20nM
BindingDB: IC50=20nM
Enzymatic activity
Enzyme Commision number 2.1.1.360: [histone H3]-lysine(79) N-trimethyltransferase.
Gene Ontology
Molecular Function
GO:0031151 histone H3K79 methyltransferase activity
Biological Process
GO:0051726 regulation of cell cycle

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5dry, PDBe:5dry, PDBj:5dry
PDBsum5dry
PubMed27563395
UniProtQ8TEK3|DOT1L_HUMAN Histone-lysine N-methyltransferase, H3 lysine-79 specific (Gene Name=DOT1L)

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