SMTL ID : 9c1q.1

Crystal structure of the WDR domain of human DCAF1 in complex with OICR-39512 compound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x 01: (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(3-methoxyprop-1-yn-1-yl)-1H-pyrrole-3-carboxamide

01.1: 19 residues within 4Å: Chain A: T.64, H.65, Y.106, R.150, C.152, R.223, V.224, V.225, Y.234, G.235, A.236, L.238, M.251, P.254, F.255, I.279, F.280, D.281, L.282 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.223, A:V.225, A:L.238, A:P.254, A:F.255 Hydrogen bonds: A:H.65, A:R.223, A:F.280, A:D.281 pi-Stacking: A:F.255 Halogen bonds: A:R.150

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

UNX.2: 3 residues within 4Å: Chain A: H.105, N.151, C.152 No protein-ligand interaction detected (PLIP) UNX.3: 2 residues within 4Å: Chain A: Y.56, N.57 No protein-ligand interaction detected (PLIP) UNX.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.5: 4 residues within 4Å: Chain A: T.138, L.139, F.140, W.169 No protein-ligand interaction detected (PLIP)

2 x NA: SODIUM ION(Non-functional Binders)

NA.6: 6 residues within 4Å: Chain A: T.39, G.40, Q.41, N.57, H.59, N.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.41, A:N.57, A:H.59 NA.7: 2 residues within 4Å: Chain A: S.9, F.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.48

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 4 residues within 4Å: Chain A: N.184, M.185, N.186, Q.221 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain A: R.250, K.252, S.253, N.296, S.299, M.300 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: S.61, A.62, T.80, W.81 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: A.14, Q.51, E.52 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

kimani, S. et al., Crystal structure of the WDR domain of human DCAF1 in complex with OICR-39512 compound. To be published

Release Date

2024-08-07

Peptides

DDB1- and CUL4-associated factor 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DDB1- and CUL4-associated factor 1

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