SMTL ID : 8g3x.1

MBP-Mcl1 in complex with ligand 32

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.63, A:R.67, A:R.67, A:Y.156, A:R.345 Water bridges: A:D.66, A:R.345

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

EDO.2: 6 residues within 4Å: Chain A: E.23, V.24, K.27, E.289, G.290, A.293 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.23 Water bridges: A:E.289, A:A.293 EDO.3: 7 residues within 4Å: Chain A: V.197, I.200, K.201, A.351, A.352, S.353, G.354 2 PLIP interactions: 2 interactions with chain A Water bridges: A:I.200, A:K.201 EDO.4: 6 residues within 4Å: Chain A: K.16, G.17, Y.18, N.19, D.297, K.298 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.18, A:N.19, A:D.297, A:K.298 Water bridges: A:K.298 EDO.5: 3 residues within 4Å: Chain A: W.11, P.41, K.47 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: D.288, E.289, E.292, Y.308, E.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.311 Water bridges: A:E.289 EDO.7: 6 residues within 4Å: Chain A: A.97, Y.177, I.330, M.331, P.332, N.333 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.65, A:N.333 Water bridges: A:N.333, A:N.333 EDO.8: 5 residues within 4Å: Chain A: K.128, V.247, L.248, P.249, T.250 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.248, A:T.250 EDO.9: 4 residues within 4Å: Chain A: Q.336, A.339, Y.372, V.496 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.368, A:Y.372, A:Y.372 EDO.10: 3 residues within 4Å: Chain A: Q.386, D.415, K.473 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.386, A:D.415, A:K.473 EDO.11: 2 residues within 4Å: Chain A: K.363, S.399 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.363, A:S.399 Water bridges: A:K.363, A:S.399

1 x YLF: N-[(1'S,3aS,5R,15S,17S,19Z,21R,21aR)-6'-chloro-20-fluoro-21-{[(5S,9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]methyl}-21-methoxy-17-methyl-13,15-dioxo-2,3,3',3a,4,4',13,16,17,18,21,21a-dodecahydro-2'H,6H,8H-15lambda~6~-spiro[10,12-(ethanediylidene)-15lambda~6~-furo[3,2-i][1,4]oxazepino[3,4-f][1,2,7]thiadiazacyclohexadecine-7,1'-naphthalen]-15-yl]-3-methoxy-1-methyl-1H-pyrazole-4-carboxamide(Non-covalent)

YLF.12: 18 residues within 4Å: Chain A: V.417, 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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.432, A:V.446, A:V.450, A:V.450, A:F.451, A:T.463, A:T.463, A:L.464, A:F.467, A:F.467 Hydrogen bonds: A:T.463 Water bridges: A:R.460, A:R.460, A:R.460 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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