SMTL ID : 5i8g.1

CBP in complex with Cpd637 ((R)-4-methyl-6-(1-methyl-3-(1-methyl-1H-pyrazol-4-yl)-1H-indazol-5-yl)-1,3,4,5-tetrahydro-2H-benzo[b][1,4]diazepin-2-one)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 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: 4 residues within 4Å: Chain A: C.165, C.171, C.189, C.192 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.165, A:C.171, A:C.189, A:C.192

1 x 69E: (4R)-4-methyl-6-[1-methyl-3-(1-methyl-1H-pyrazol-4-yl)-1H-indazol-5-yl]-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one(Non-covalent)

69E.4: 13 residues within 4Å: Chain A: L.61, P.62, F.63, Q.65, V.67, L.72, Y.77, Y.119, N.120, R.125, V.126, F.129 Ligands: PEG.12 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.62, A:F.63, A:L.72, A:V.126 Hydrogen bonds: A:P.62, A:N.120, A:N.120

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

B3P.5: 8 residues within 4Å: Chain A: W.110, N.114, W.117, Y.156, D.225, T.226, L.227 Ligands: EDO.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.117 Hydrogen bonds: A:N.114, A:Y.156, A:D.225, A:L.227 Water bridges: A:Y.127, A:Y.127

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

EDO.6: 5 residues within 4Å: Chain A: K.93, Q.98, Y.99, Q.104, D.108 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.93, A:Q.98 Water bridges: A:K.93, A:D.108, A:D.108 EDO.7: 4 residues within 4Å: Chain A: W.117, Y.127, S.131 Ligands: B3P.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.127 EDO.8: 5 residues within 4Å: Chain A: V.233, L.248, W.254, G.257, F.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.258 Water bridges: A:G.257 EDO.9: 6 residues within 4Å: Chain A: P.39, E.40, R.43, L.94, D.95, G.97 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.40, A:E.40, A:G.97 Water bridges: A:R.43, A:D.95, A:T.96 EDO.10: 4 residues within 4Å: Chain A: H.249, Y.250, D.251, I.252 No protein-ligand interaction detected (PLIP)

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

NA.11: 2 residues within 4Å: Chain A: R.125, K.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.125

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

PEG.12: 2 residues within 4Å: Chain A: L.72 Ligands: 69E.4 No protein-ligand interaction detected (PLIP) PEG.13: 6 residues within 4Å: Chain A: L.50, E.51, Y.54, L.87, S.88, K.91 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.87

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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