SMTL ID : 7vun.1

Design, modification, evaluation and cocrystal studies of novel phthalimides regulating PD-1/PD-L1 interaction

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-octamer

Ligands

4 x 8H7: (2~{S},3~{S})-2-[[6-[(3-cyanophenyl)methoxy]-2-(2-methyl-3-phenyl-phenyl)-1,3-bis(oxidanylidene)isoindol-5-yl]methylamino]-3-oxidanyl-butanoic acid(Non-covalent)

8H7.1: 19 residues within 4Å: Chain C: F.2, T.3, I.37, Y.39, M.98, I.99, S.100, A.104, D.105, Y.106, K.107, R.108 Chain E: I.37, Y.39, M.98, I.99, S.100, A.104, D.105 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain E Hydrophobic interactions: C:I.37, C:M.98, C:A.104, C:Y.106, C:K.107, E:I.37, E:Y.39, E:M.98, E:A.104 Hydrogen bonds: C:D.105, C:R.108 Water bridges: C:A.104 Salt bridges: C:K.107 pi-Stacking: C:Y.39, E:Y.39, E:Y.39 pi-Cation interactions: C:K.107 8H7.2: 20 residues within 4Å: Chain D: F.2, T.3, I.37, Y.39, M.98, I.99, S.100, A.104, D.105, Y.106, K.107, R.108 Chain G: I.37, Y.39, Q.49, M.98, I.99, S.100, A.104, D.105 18 PLIP interactions: 6 interactions with chain G, 12 interactions with chain D Hydrophobic interactions: G:I.37, G:Y.39, G:M.98, G:A.104, D:T.3, D:I.37, D:M.98, D:A.104, D:Y.106, D:Y.106 pi-Stacking: G:Y.39, G:Y.39, D:Y.39 Hydrogen bonds: D:F.2, D:D.105, D:K.107, D:R.108 Salt bridges: D:K.107 8H7.3: 9 residues within 4Å: Chain F: I.37, Y.39, M.98, S.100, A.104, D.105, Y.106, K.107, R.108 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:I.37, F:Y.39, F:M.98, F:A.104 Hydrogen bonds: F:R.108, F:R.108 pi-Stacking: F:Y.39 pi-Cation interactions: F:K.107 8H7.4: 19 residues within 4Å: Chain A: I.37, Y.39, Q.49, M.98, I.99, S.100, A.104, D.105 Chain H: F.2, T.3, I.37, Y.39, M.98, S.100, A.104, D.105, Y.106, K.107, R.108 16 PLIP interactions: 10 interactions with chain H, 6 interactions with chain A Hydrophobic interactions: H:I.37, H:M.98, H:A.104, H:Y.106, A:I.37, A:Y.39, A:M.98, A:A.104 Hydrogen bonds: H:D.105, H:D.105, H:R.108 Salt bridges: H:K.107 pi-Stacking: H:Y.39, A:Y.39, A:Y.39 pi-Cation interactions: H:K.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, C. et al., Novel phthalimides regulating PD-1/PD-L1 interaction as potential immunotherapy agents. Acta Pharm Sin B (2022)

Release Date

2022-09-14

Peptides

Programmed cell death 1 ligand 1: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
D

E
E

F
F

G
G

H
H

Programmed cell death 1 ligand 1

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