Structure of PDB 4ek9 Chain A Binding Site BS01

Receptor Information
>4ek9 Chain A (length=325) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLA
MENYDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLL
RHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDD
LFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMK
WYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERF
ANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVSWTG
KPVSYYLHTIDRTILENYFSSLKNP
Ligand information
Ligand IDEP4
InChIInChI=1S/C12H18N6O3/c1-17(2)3-6-8(19)9(20)12(21-6)18-5-16-7-10(13)14-4-15-11(7)18/h4-6,8-9,12,19-20H,3H2,1-2H3,(H2,13,14,15)/t6-,8-,9-,12-/m1/s1
InChIKeySLNWRDWGFHZRAQ-WOUKDFQISA-N
SMILES
SoftwareSMILES
CACTVS 3.370CN(C)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 12.01n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CN(C)C)N
OpenEye OEToolkits 1.7.6CN(C)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
OpenEye OEToolkits 1.7.6CN(C)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.370CN(C)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
FormulaC12 H18 N6 O3
Name5'-deoxy-5'-(dimethylamino)adenosine
ChEMBLCHEMBL472733
DrugBank
ZINCZINC000040914070
PDB chain4ek9 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ek9 Conformational adaptation drives potent, selective and durable inhibition of the human protein methyltransferase DOT1L.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		P133 G137 G163 E186 K187 G221 D222 F223
Binding residue
(residue number reindexed from 1)		P126 G130 G156 E179 K180 G214 D215 F216
Annotation score2
Binding affinityMOAD: Ki=38000nM
PDBbind-CN: -logKd/Ki=4.42,Ki=38000nM
BindingDB: Ki=9000nM
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:4ek9, PDBe:4ek9, PDBj:4ek9
PDBsum4ek9
PubMed22978415
UniProtQ8TEK3|DOT1L_HUMAN Histone-lysine N-methyltransferase, H3 lysine-79 specific (Gene Name=DOT1L)

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