Structure of PDB 2ydw Chain B Binding Site BS01

Receptor Information

>2ydw Chain B (length=105) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

NQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTI
KRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQK
VASMP

Ligand information

Ligand ID

WSH

InChI

InChI=1S/C25H21N5O2/c1-17-28-29-24-23(27-25(31)32-16-18-10-4-2-5-11-18)26-22(19-12-6-3-7-13-19)20-14-8-9-15-21(20)30(17)24/h2-15,23H,16H2,1H3,(H,27,31)/t23-/m0/s1

InChIKey

TUWDLUFFAHHNEF-QHCPKHFHSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.0	Cc1nnc2n1-c3ccccc3C(=NC2NC(=O)OCc4ccccc4)c5ccccc5
CACTVS 3.370	Cc1nnc2[CH](NC(=O)OCc3ccccc3)N=C(c4ccccc4)c5ccccc5n12
CACTVS 3.370	Cc1nnc2[C@H](NC(=O)OCc3ccccc3)N=C(c4ccccc4)c5ccccc5n12
OpenEye OEToolkits 1.7.0	Cc1nnc2n1-c3ccccc3C(=N[C@H]2NC(=O)OCc4ccccc4)c5ccccc5
ACDLabs 12.01	O=C(OCc1ccccc1)NC4N=C(c2ccccc2n3c4nnc3C)c5ccccc5

Formula

C25 H21 N5 O2

Name

BENZYL [(4R)-1-METHYL-6-PHENYL-4H-[1,2,4]TRIAZOLO[4,3-A][1,4]BENZODIAZEPIN-4-YL]CARBAMATE

PDB chain

2ydw Chain B Residue 1182 [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	2ydw Discovery and Characterization of Small Molecule Inhibitors of the Bet Family Bromodomains.
Resolution	1.9 Å
Binding residue (original residue number in PDB)	W97 P98 V103 L108 L110 Y155 N156 I162
Binding residue (residue number reindexed from 1)	W21 P22 V27 L32 L34 Y79 N80 I86
Annotation score	1
Binding affinity	MOAD: Kd=46nM PDBbind-CN: -logKd/Ki=7.34,Kd=46.0nM BindingDB: Kd=52nM,IC50=29.9nM

Enzymatic activity

Enzyme Commision number

External links

PDB	RCSB:2ydw, PDBe:2ydw, PDBj:2ydw
PDBsum	2ydw
PubMed	21568322
UniProt	P25440\|BRD2_HUMAN Bromodomain-containing protein 2 (Gene Name=BRD2)

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