SMTL ID : 9ejq.1

Crystal structure of DDB1 in complex with XS381952

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

monomer

Ligands

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.1: 5 residues within 4Å: Chain A: I.222, H.263, N.264, R.265, Y.273 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.264, A:R.265 Water bridges: A:K.170, A:A.223, A:A.223, A:H.263, A:H.263, A:H.263 Salt bridges: A:H.263, A:R.265 TLA.2: 6 residues within 4Å: Chain A: R.416, N.464, V.465, A.466, H.467, Q.468 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.465, A:H.467, A:Q.468, A:Q.469 Water bridges: A:N.464, A:V.465 Salt bridges: A:R.416

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: K.866, E.867, R.891 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.903 Water bridges: A:K.866, A:R.891, A:R.891, A:T.903 GOL.4: 6 residues within 4Å: Chain A: E.877, F.878, N.879, T.918, K.919, G.920 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.877, A:N.879, A:T.918, A:G.920 Water bridges: A:G.880, A:G.920 GOL.10: 6 residues within 4Å: Chain A: G.331, D.332, E.386, S.388, R.390, P.718 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.332 Water bridges: A:L.719 GOL.11: 5 residues within 4Å: Chain A: T.10, L.1002, E.1004, R.1076, D.1094 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.1004, A:R.1076, A:R.1076, A:D.1094 Water bridges: A:N.38, A:R.40, A:D.1092 GOL.12: 5 residues within 4Å: Chain A: K.725, Y.915, S.957, F.1005, N.1007 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.725, A:K.725, A:Y.915, A:N.1007 Water bridges: A:Y.915 GOL.14: 6 residues within 4Å: Chain A: R.715, T.716, V.717, P.718, T.800, F.801 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.715, A:R.715, A:F.801

1 x 01: (4S)-4-(3-ethoxyphenyl)-3-methyl-1-[(4R)-[1,2,4]triazolo[4,3-b]pyridazin-6-yl]-1,4,5,7-tetrahydro-6H-pyrazolo[3,4-b]pyridin-6-one

01.5: 13 residues within 4Å: Chain A: P.1025, S.1048, W.1049, L.1052, Y.1116, D.1117, D.1118, G.1119, D.1130, L.1131, K.1133, V.1134, E.1137 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:P.1025, A:L.1052, A:Y.1116, A:Y.1116, A:D.1130, A:L.1131, A:K.1133, A:E.1137 Hydrogen bonds: A:S.1048 Water bridges: A:S.1046 pi-Stacking: A:W.1049, A:W.1049, A:W.1049, A:Y.1116

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

EDO.6: 4 residues within 4Å: Chain A: N.18, N.38, K.62, N.1036 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.18, A:N.38, A:K.62, A:N.1036 Water bridges: A:N.1036 EDO.7: 3 residues within 4Å: Chain A: V.454, D.455, D.456 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.455, A:D.455 EDO.8: 3 residues within 4Å: Chain A: F.461, S.504, C.505 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.505 Water bridges: A:C.505, A:T.546 EDO.9: 4 residues within 4Å: Chain A: C.365, V.366, V.367, Y.728 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.366 Water bridges: A:Y.728 EDO.13: 4 residues within 4Å: Chain A: S.490, E.491, W.492, L.528 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.491

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

SO4.15: 7 residues within 4Å: Chain A: N.18, G.19, A.36, I.63, A.64, V.65, M.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.66 Water bridges: A:E.67 SO4.16: 8 residues within 4Å: Chain A: Q.729, V.731, S.732, N.828, T.829, Q.854, Y.855, S.856 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.829, A:Q.854 Water bridges: A:Y.855, A:Y.855 SO4.17: 6 residues within 4Å: Chain A: I.35, K.37, E.42, Y.44, F.325, F.355 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.44 Water bridges: A:K.37, A:K.37 Salt bridges: A:K.37 SO4.18: 6 residues within 4Å: Chain A: G.58, Y.60, I.1064, K.1065, S.1066, V.1067 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.1067 Water bridges: A:Y.60 SO4.19: 3 residues within 4Å: Chain A: E.67, I.125, I.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.67, A:I.126, A:I.126 SO4.20: 5 residues within 4Å: Chain A: R.70, K.72, P.128, E.129, C.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.70, A:K.72 SO4.21: 5 residues within 4Å: Chain A: T.120, I.123, I.167, D.168, S.219 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.120, A:D.168 Water bridges: A:V.221

5 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.22: 2 residues within 4Å: Chain A: L.68, D.77 No protein-ligand interaction detected (PLIP) UNX.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.24: 3 residues within 4Å: Chain A: A.313, E.314, R.329 No protein-ligand interaction detected (PLIP) UNX.25: 2 residues within 4Å: Chain A: S.764, S.765 No protein-ligand interaction detected (PLIP) UNX.26: 3 residues within 4Å: Chain A: E.309, S.347, V.349 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, H. et al., Crystal structure of DDB1 in complex with XS381952. To be published

Release Date

2025-02-26

Peptides

DNA damage-binding protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA damage-binding protein 1