SMTL ID : 5vkc.1

Crystal structure of MCL-1 in complex with a BIM competitive inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-dimer

Ligands

2 x 9EA: 7-(3-{[4-(4-acetylpiperazin-1-yl)phenoxy]methyl}-1,5-dimethyl-1H-pyrazol-4-yl)-3-{3-[(naphthalen-1-yl)oxy]propyl}-1-[(pyridin-3-yl)methyl]-1H-indole-2-carboxylic acid(Non-covalent)

9EA.1: 19 residues within 4Å: Chain A: V.51, H.55, A.58, F.59, M.62, L.66, M.81, V.84, F.85, G.93, R.94, T.97, L.98, F.101, G.102, I.125, F.150 Ligands: ZN.2, ZN.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.59, A:L.66, A:V.84, A:F.85, A:T.97, A:T.97, A:L.98, A:F.101, A:F.101, A:I.125, A:F.150 Water bridges: A:G.93 Salt bridges: A:R.94 pi-Stacking: A:H.55, A:F.101, A:F.101 9EA.9: 21 residues within 4Å: Chain A: H.151 Chain B: V.47, V.51, H.55, A.58, F.59, M.62, L.66, M.81, V.84, F.85, G.93, R.94, T.97, L.98, F.101, G.102, I.125, F.150 Ligands: ZN.8, ZN.10 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:V.47, B:F.59, B:F.59, B:L.66, B:V.84, B:F.85, B:T.97, B:L.98, B:F.101, B:I.125, B:F.150 Hydrogen bonds: B:V.84 Water bridges: B:G.93 Salt bridges: B:R.94 pi-Stacking: B:H.55, B:F.101, B:F.101, B:F.101

10 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.2: 2 residues within 4Å: Chain A: H.55 Ligands: 9EA.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.55 ZN.3: 1 residues within 4Å: Ligands: 9EA.1 No protein-ligand interaction detected (PLIP) ZN.4: 2 residues within 4Å: Chain A: H.83, D.87 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.83, A:D.87, H2O.2 ZN.5: 2 residues within 4Å: Chain A: R.79, H.83 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.83, H2O.1 ZN.6: 1 residues within 4Å: Chain A: D.73 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.73 ZN.7: 1 residues within 4Å: Chain A: D.72 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.72 ZN.8: 2 residues within 4Å: Chain A: H.151 Ligands: 9EA.9 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.151, H2O.2, H2O.4 ZN.10: 2 residues within 4Å: Chain B: H.55 Ligands: 9EA.9 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.55, H2O.3 ZN.11: 2 residues within 4Å: Chain B: R.79, H.83 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.83, H2O.4 ZN.12: 3 residues within 4Å: Chain A: E.153 Chain B: H.83, D.87 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.83, B:D.87, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bruncko, M. et al., Structure-guided design of a series of MCL-1 inhibitors with high affinity and selectivity. J. Med. Chem. (2015)

Release Date

2017-05-03

Peptides

Induced myeloid leukemia cell differentiation protein Mcl-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Induced myeloid leukemia cell differentiation protein Mcl-1

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