Structure of PDB 6u9k Chain B Binding Site BS02

Receptor Information

>6u9k Chain B (length=149) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

LPMPMRFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGIVI
RSILTDKREKYYDSKGIGCYMFRIDDSEVVDATMHGNAARFINHSCEPNC
YSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFKLPCNCGAKKCRKFLN

Ligand information

Ligand ID

Q2V

InChI

InChI=1S/C33H42N8O5/c34-25(33(44)45)12-14-40(18-26-28(42)29(43)32(46-26)41-20-38-27-30(35)36-19-37-31(27)41)17-21-15-39(16-21)13-11-24(22-7-3-1-4-8-22)23-9-5-2-6-10-23/h1-10,19-21,24-26,28-29,32,42-43H,11-18,34H2,(H,44,45)(H2,35,36,37)/t25-,26+,28+,29+,32+/m0/s1

InChIKey

VHPRRJZGFMSHQV-JUCHKJSUSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.7	c1ccc(cc1)C(CCN2CC(C2)CN(CC[C@@H](C(=O)O)N)C[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)c6ccccc6
CACTVS 3.385	N[C@@H](CCN(CC1CN(CCC(c2ccccc2)c3ccccc3)C1)C[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)C(O)=O
ACDLabs 12.01	n6cnc5n(C4OC(CN(CC3CN(CCC(c1ccccc1)c2ccccc2)C3)CCC(C(=O)O)N)C(C4O)O)cnc5c6N
OpenEye OEToolkits 2.0.7	c1ccc(cc1)C(CCN2CC(C2)CN(CCC(C(=O)O)N)CC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)c6ccccc6
CACTVS 3.385	N[CH](CCN(CC1CN(CCC(c2ccccc2)c3ccccc3)C1)C[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)C(O)=O

Formula

C33 H42 N8 O5

Name

5'-([(3S)-3-amino-3-carboxypropyl]{[1-(3,3-diphenylpropyl)azetidin-3-yl]methyl}amino)-5'-deoxyadenosine

PDB chain

6u9k Chain B Residue 4003 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	6u9k Discovery of Potent Small-Molecule Inhibitors of MLL Methyltransferase.
Resolution	2.0 Å
Binding residue (original residue number in PDB)	I3838 H3839 R3841 G3881 C3882 Y3883 F3904 N3906 H3907 Y3944 C3957 N3958
Binding residue (residue number reindexed from 1)	I25 H26 R28 G68 C69 Y70 F91 N93 H94 Y131 C137 N138
Annotation score	2
Binding affinity	MOAD: ic50=138.4nM

Enzymatic activity

Catalytic site (original residue number in PDB)	Y3858 Y3944
Catalytic site (residue number reindexed from 1)	Y45 Y131
Enzyme Commision number	2.1.1.- 2.1.1.364: [histone H3]-lysine(4) N-methyltransferase.

External links

PDB	RCSB:6u9k, PDBe:6u9k, PDBj:6u9k
PDBsum	6u9k
PubMed	32551023
UniProt	Q03164\|KMT2A_HUMAN Histone-lysine N-methyltransferase 2A (Gene Name=KMT2A)

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