SMTL ID : 5i8b.1

CBP in complex with Cpd23 ((R)-6-(3-(benzyloxy)phenyl)-4-methyl-1,3,4,5-tetrahydro-2H-benzo[b][1,4]diazepin-2-one)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.151, C.152, H.243, C.246 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.151, A:C.152, A:H.243, A:C.246 ZN.2: 4 residues within 4Å: Chain A: C.235, C.238, C.260, C.263 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.235, A:C.238, A:C.260, A:C.263 ZN.3: 5 residues within 4Å: Chain A: C.165, C.171, F.188, C.189, C.192 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.165, A:C.171, A:C.189

1 x 69F: (4R)-6-[3-(benzyloxy)phenyl]-4-methyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one(Non-covalent)

69F.4: 12 residues within 4Å: Chain A: L.61, P.62, Q.65, V.67, L.72, I.74, Y.77, Y.119, N.120, R.125, V.126 Ligands: EDO.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.61, A:P.62, A:L.72, A:I.74, A:V.126 Hydrogen bonds: A:P.62, A:N.120, A:N.120 pi-Cation interactions: A:R.125

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.5: 10 residues within 4Å: Chain A: W.110, N.114, W.117, Y.127, S.131, Y.156, D.225, T.226, L.227 Ligands: EDO.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.117 Hydrogen bonds: A:N.114, A:Y.127, A:S.131, A:Y.156, A:D.225, A:L.227

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 1 residues within 4Å: Ligands: 69F.4 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: R.33, E.237, C.263 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.33, A:C.263 Water bridges: A:E.237 EDO.8: 2 residues within 4Å: Chain A: S.32, R.33 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.32, A:K.34 EDO.9: 3 residues within 4Å: Chain A: D.225, T.226 Ligands: B3P.5 No protein-ligand interaction detected (PLIP) EDO.10: 3 residues within 4Å: Chain A: E.51, Y.54, K.91 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 3 residues within 4Å: Chain A: W.117, L.118, N.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.120 Water bridges: A:K.122

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 5 residues within 4Å: Chain A: K.93, Q.98, Y.99, Q.104, D.108 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.93, A:Q.98 Water bridges: A:K.93, A:Q.98, A:D.108, A:D.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taylor, A.M. et al., Fragment-Based Discovery of a Selective and Cell-Active Benzodiazepinone CBP/EP300 Bromodomain Inhibitor (CPI-637). Acs Med.Chem.Lett. (2016)

Release Date

2016-04-20

Peptides

CREB-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CREB-binding protein

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