SMTL ID : 8ojh.1

Crystal structure of human CRBN-DDB1 in complex with compound 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: T.13, K.35, E.40, Y.42, S.331, F.353, T.354 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.35, A:S.331, A:T.354 Water bridges: A:S.331 EDO.2: 7 residues within 4Å: Chain A: G.56, M.57, Y.58, I.1062, K.1063, S.1064, V.1065 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.1064, A:V.1065 Water bridges: A:Y.58 EDO.3: 5 residues within 4Å: Chain A: G.329, D.330, E.384, R.388, P.716 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.330 Water bridges: A:E.384, A:G.385, A:R.388 EDO.4: 8 residues within 4Å: Chain A: L.960, H.1009, Q.1025, G.1026, S.1027, V.1028, T.1041, S.1042 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.960, A:Q.1025 Water bridges: A:M.1 EDO.5: 5 residues within 4Å: Chain A: I.100, I.101, T.102, S.1064, V.1065 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.102, A:T.102, A:S.1064 EDO.6: 5 residues within 4Å: Chain A: I.88, R.103, L.145, D.146, N.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.103, A:N.149 EDO.7: 4 residues within 4Å: Chain A: E.160, E.161, L.162, D.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.162, A:D.184 Water bridges: A:H.163 EDO.10: 6 residues within 4Å: Chain B: Q.51, M.53, M.54, G.319, Y.320, V.321 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.51, B:M.53, B:M.54, B:V.321 EDO.11: 3 residues within 4Å: Chain B: P.389, T.390, I.391 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.391

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain B: C.288, C.291, C.356, C.359 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.288, B:C.291, B:C.356, B:C.359

1 x VP9: 4-azanyl-2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-7-methoxy-isoindole-1,3-dione(Non-covalent)

VP9.9: 10 residues within 4Å: Chain B: N.316, P.317, H.318, E.342, H.343, S.344, W.345, W.351, W.365, F.367 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:P.317, B:W.345, B:W.351, B:W.351, B:W.351, B:W.365, B:W.365 Hydrogen bonds: B:N.316, B:E.342, B:H.343, B:W.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bouguenina, H. et al., A Degron Blocking Strategy Towards Improved CRL4 CRBN Recruiting PROTAC Selectivity. Chembiochem (2023)

Release Date

2023-07-19

Peptides

DNA damage-binding protein 1: A
Protein cereblon: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA damage-binding protein 1

Protein cereblon

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