Structure of PDB 6cd4 Chain A Binding Site BS01

Receptor Information

>6cd4 Chain A (length=124) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

TNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKL
NLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKP
GDDIVLMAEALEKLFLQKINELPT

Ligand information

Ligand ID

EX1

InChI

InChI=1S/C33H42N8O3/c1-22(2)41-27-9-7-6-8-25(27)32(43)38(4)28-21-34-33(36-30(28)41)35-26-11-10-23(20-29(26)44-5)31(42)40-14-12-24(13-15-40)39-18-16-37(3)17-19-39/h6-11,20-22,24H,12-19H2,1-5H3,(H,34,35,36)

InChIKey

MARFRTLFUBVKOT-UHFFFAOYSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.6	CC(C)N1c2ccccc2C(=O)N(c3c1nc(nc3)Nc4ccc(cc4OC)C(=O)N5CCC(CC5)N6CCN(CC6)C)C
ACDLabs 12.01	C1(CCN(CC1)C(=O)c2ccc(c(OC)c2)Nc5nc3c(N(C(=O)c4c(N3C(C)C)cccc4)C)cn5)N6CCN(CC6)C
CACTVS 3.385	COc1cc(ccc1Nc2ncc3N(C)C(=O)c4ccccc4N(C(C)C)c3n2)C(=O)N5CCC(CC5)N6CCN(C)CC6

Formula

C33 H42 N8 O3

Name

2-({2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-11-(propan-2-yl)-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one

ChEMBL

DrugBank

ZINC

PDB chain

6cd4 Chain A Residue 201 [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	6cd4 Structural and Atropisomeric Factors Governing the Selectivity of Pyrimido-benzodiazipinones as Inhibitors of Kinases and Bromodomains.
Resolution	1.23 Å
Binding residue (original residue number in PDB)	W81 P82 L92 L94 Y139 I146
Binding residue (residue number reindexed from 1)	W39 P40 L50 L52 Y97 I104
Annotation score	1
Binding affinity	MOAD: ic50=5.14uM PDBbind-CN: -logKd/Ki=5.34,IC50=4.59uM

Enzymatic activity

Enzyme Commision number

External links

PDB	RCSB:6cd4, PDBe:6cd4, PDBj:6cd4
PDBsum	6cd4
PubMed	30102854
UniProt	O60885\|BRD4_HUMAN Bromodomain-containing protein 4 (Gene Name=BRD4)

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