SMTL ID : 6uvd.1

Crystal structure of BCL-XL bound to compound 2: (2R)-3-(Benzylsulfanyl)-2-({[(4-methylphenyl)methyl] [(4 phenylphenyl)carbonyl] carbamoyl}amino) propanoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x XOU: (2R)-3-(Benzylsulfanyl)-2-({[(4-methylphenyl)methyl] [(4 phenylphenyl)carbonyl] carbamoyl}amino) propanoic acid(Non-covalent)

XOU.1: 18 residues within 4Å: Chain A: A.42, E.45, F.46, R.49, Y.50, A.53, F.54, L.57, L.79, N.85, W.86, G.87, R.88, V.90, A.91, F.140, Y.144 Ligands: EDO.9 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.42, A:E.45, A:F.46, A:F.46, A:F.46, A:Y.50, A:A.53, A:L.57, A:W.86, A:V.90, A:A.91, A:F.140, A:Y.144, A:Y.144, A:Y.144 Hydrogen bonds: A:N.85 Water bridges: A:R.88 pi-Stacking: A:F.46 XOU.11: 14 residues within 4Å: Chain B: F.46, Y.50, A.53, D.56, L.57, Q.60, E.78, L.79, G.87, R.88, A.91, Y.144 Ligands: EDO.12, EDO.13 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.46, B:F.46, B:Y.50, B:A.53, B:E.78, B:A.91 Salt bridges: B:R.88 pi-Stacking: B:Y.50

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.49, Y.50, R.51, R.52, A.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.52, A:A.53 Salt bridges: A:R.52 SO4.3: 5 residues within 4Å: Chain A: Y.20, S.23, Q.24, Q.37, E.41 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.23, A:Q.37, A:E.41 Water bridges: A:Q.24, A:Q.24 SO4.4: 3 residues within 4Å: Chain A: R.11, W.29 Chain B: S.113 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Water bridges: B:S.113, B:S.113, A:R.11, A:R.11 Salt bridges: A:R.11

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

EDO.5: 5 residues within 4Å: Chain A: F.80, V.84, Y.122, H.126, L.127 No protein-ligand interaction detected (PLIP) EDO.6: 2 residues within 4Å: Chain A: D.125, P.129 No protein-ligand interaction detected (PLIP) EDO.7: 5 residues within 4Å: Chain A: P.65, E.107, M.108, Q.109, V.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.109, A:V.110 EDO.8: 4 residues within 4Å: Chain A: E.47, R.51, A.98 Chain B: K.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.51, A:G.97 EDO.9: 3 residues within 4Å: Chain A: E.45, Y.144 Ligands: XOU.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.45 Water bridges: A:Y.144 EDO.10: 4 residues within 4Å: Chain A: D.82, G.83, N.85, R.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.84, A:N.85 EDO.12: 3 residues within 4Å: Chain B: N.85, R.88 Ligands: XOU.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.85, B:R.88, B:R.88 EDO.13: 7 residues within 4Å: Chain B: E.78, L.79, F.80, R.81, D.82, R.88 Ligands: XOU.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.82, B:D.82 EDO.14: 3 residues within 4Å: Chain B: T.64, P.65, G.66 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.64, B:G.66 EDO.15: 6 residues within 4Å: Chain B: S.23, G.26, Y.27, S.28, A.33, A.34 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.23 Water bridges: B:G.26, B:S.28 EDO.16: 2 residues within 4Å: Chain B: V.84, W.130 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roy, M.J. et al., Structure-Guided Development of Potent Benzoylurea Inhibitors of BCL-X L and BCL-2. J.Med.Chem. (2021)

Release Date

2021-05-05

Peptides

Bcl-2-like protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bcl-2-like protein 1

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