Structure of PDB 5dt2 Chain B Binding Site BS01

Receptor Information
>5dt2 Chain B (length=315) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKL
AMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTLNTRPSTGLLR
HILQQVYNHSVTDPEKPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLG
SGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKH
AEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEG
GRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKVSWTGKPVSYYLH
TIDRTILENYFSSLK
Ligand information
Ligand ID5EV
InChIInChI=1S/C26H23N5O/c1-18-16-19-12-13-20(29-26-28-15-14-25(27-2)30-26)17-23(19)31(18)22-10-6-7-11-24(22)32-21-8-4-3-5-9-21/h3-17H,1-2H3,(H2,27,28,29,30)
InChIKeyVTOOSSZNUMLKNN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2Cc1cc2ccc(cc2n1c3ccccc3Oc4ccccc4)Nc5nccc(n5)NC
CACTVS 3.385CNc1ccnc(Nc2ccc3cc(C)n(c4ccccc4Oc5ccccc5)c3c2)n1
ACDLabs 12.01c25c(cc(Nc1nc(ccn1)NC)cc2)n(c3c(cccc3)Oc4ccccc4)c(c5)C
FormulaC26 H23 N5 O
NameN~4~-methyl-N~2~-[2-methyl-1-(2-phenoxyphenyl)-1H-indol-6-yl]pyrimidine-2,4-diamine
ChEMBLCHEMBL4577516
DrugBank
ZINCZINC000584904964
PDB chain5dt2 Chain B Residue 401 [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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PDB5dt2 Discovery of Novel Dot1L Inhibitors through a Structure-Based Fragmentation Approach.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		F131 S140 L143 V144 M147 D161 S164 V169 F239 V240 N241 F243 S268 S269
Binding residue
(residue number reindexed from 1)		F118 S127 L130 V131 M134 D148 S151 V156 F226 V227 N228 F230 S255 S256
Annotation score1
Binding affinityMOAD: ic50=150nM
BindingDB: IC50=150nM
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:5dt2, PDBe:5dt2, PDBj:5dt2
PDBsum5dt2
PubMed27563395
UniProtQ8TEK3|DOT1L_HUMAN Histone-lysine N-methyltransferase, H3 lysine-79 specific (Gene Name=DOT1L)

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