SMTL ID : 8g3t.1

MBP-Mcl1 in complex with ligand 12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

monomer

Ligands

1 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 16 residues within 4Å: Chain A: N.13, D.15, K.16, W.63, A.64, D.66, R.67, E.112, E.154, P.155, Y.156, F.157, W.231, M.331, W.341, R.345 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.63, A:R.67, A:R.67, A:E.154, A:Y.156, A:R.345 Water bridges: A:E.45, A:R.67

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 6 residues within 4Å: Chain A: V.197, I.200, K.201, A.351, A.352, G.354 No protein-ligand interaction detected (PLIP)

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

EDO.3: 5 residues within 4Å: Chain A: H.65, Y.177, M.331, P.332, N.333 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.65, A:N.333 Water bridges: A:N.333

1 x YLK: (1'S,3aS,5R,16R,17S,19Z,21R,21aR)-6'-chloro-20-fluoro-21-methoxy-16,17-dimethyl-2,3,3',3a,4',16,17,18,21,21a-decahydro-2'H,6H,8H-15lambda~6~-spiro[10,12-etheno-15lambda~6~-furo[3,2-i][1,4]oxazepino[3,4-f][1,2,7]thiadiazacyclohexadecine-7,1'-naphthalene]-13,15,15(4H,14H)-trione(Non-covalent)

YLK.4: 17 residues within 4Å: Chain A: H.421, A.424, F.425, M.428, L.432, V.446, M.447, V.450, F.451, G.459, R.460, T.463, L.464, F.467, G.468, L.487, I.491 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.432, A:V.446, A:V.450, A:F.451, A:T.463, A:T.463, A:L.464, A:F.467 Hydrogen bonds: A:R.460, A:T.463, A:T.463 Water bridges: A:T.463 pi-Stacking: A:F.467

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Romanov-Michailidis, F. et al., Discovery of an Oral, Beyond-Rule-of-Five Mcl-1 Protein-Protein Interaction Modulator with the Potential of Treating Hematological Malignancies. J.Med.Chem. (2023)

Release Date

2023-05-17

Peptides

Maltodextrin-binding protein, Induced myeloid leukemia cell differentiation protein Mcl-1 chimera: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Maltodextrin-binding protein, Induced myeloid leukemia cell differentiation protein Mcl-1 chimera

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