SMTL ID : 4wmr.2 (2 other biounits)

STRUCTURE OF MCL1 BOUND TO BRD inhibitor ligand 1 AT 1.7A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

ZN.1: 3 residues within 4Å: Chain A: H.53 Ligands: 865.4, POP.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.53 ZN.2: 3 residues within 4Å: Chain A: H.81, D.85 Ligands: POP.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.81, A:D.85 ZN.3: 3 residues within 4Å: Ligands: POP.5, ZN.9, POP.11 No protein-ligand interaction detected (PLIP) ZN.7: 3 residues within 4Å: Chain B: H.53 Ligands: 865.10, POP.11 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.53 ZN.8: 3 residues within 4Å: Chain B: H.81, D.85 Ligands: POP.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.81, B:D.85 ZN.9: 3 residues within 4Å: Ligands: ZN.3, POP.5, POP.11 No protein-ligand interaction detected (PLIP)

2 x 865: 7-[2-(1H-imidazol-1-yl)-4-methylpyridin-3-yl]-3-[3-(naphthalen-1-yloxy)propyl]-1-[2-oxo-2-(piperazin-1-yl)ethyl]-1H-indole-2-carboxylic acid(Non-covalent)

865.4: 20 residues within 4Å: Chain A: H.53, A.56, F.57, M.60, L.75, V.78, M.79, V.82, F.83, R.92, T.95, L.96, F.99, G.100, L.119, I.123 Chain B: T.55 Ligands: ZN.1, POP.5, POP.11 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.75, A:V.78, A:M.79, A:V.82, A:F.83, A:T.95, A:F.99, A:L.119, A:I.123 Water bridges: A:T.95, B:A.56 Salt bridges: A:R.92 pi-Stacking: A:F.99, A:F.99, A:F.99 865.10: 20 residues within 4Å: Chain A: T.55 Chain B: H.53, A.56, F.57, M.60, L.75, V.78, M.79, V.82, F.83, R.92, T.95, L.96, F.99, G.100, L.119, I.123 Ligands: POP.5, ZN.7, POP.11 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.75, B:V.78, B:M.79, B:V.82, B:F.83, B:T.95, B:F.99, B:L.119, B:I.123 Salt bridges: B:R.92 pi-Stacking: B:F.99, B:F.99, B:F.99 Water bridges: A:A.56

4 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.5: 7 residues within 4Å: Chain A: H.53 Ligands: ZN.1, ZN.3, 865.4, ZN.9, 865.10, POP.11 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.56 Salt bridges: A:H.53, A:H.53 POP.6: 3 residues within 4Å: Chain A: H.81, D.85 Ligands: ZN.2 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.81, A:H.81 POP.11: 7 residues within 4Å: Chain B: H.53 Ligands: ZN.3, 865.4, POP.5, ZN.7, ZN.9, 865.10 3 PLIP interactions: 3 interactions with chain B Water bridges: B:A.56 Salt bridges: B:H.53, B:H.53 POP.12: 3 residues within 4Å: Chain B: H.81, D.85 Ligands: ZN.8 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.81, B:H.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clifton, M.C. et al., A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1. Plos One (2015)

Release Date

2015-05-06

Peptides

Induced myeloid leukemia cell differentiation protein Mcl-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Induced myeloid leukemia cell differentiation protein Mcl-1

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