SMTL ID : 8t1q.1

Crystal structure of human CPSF73 catalytic segment in complex with compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x XYX: 3-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-5-yl]-~{N}-[3-(4-ethanoylphenyl)phenyl]propanamide(Non-covalent)

XYX.1: 22 residues within 4Å: Chain A: V.43, I.63, P.65, H.91, H.93, L.94, D.95, H.96, Y.130, V.133, H.178, D.199, F.261, M.351, Q.353, S.354, Y.377, V.379, H.416, H.438 Ligands: FE.5, FE.6 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.63, A:I.63, A:P.65, A:H.93, A:L.94, A:L.94, A:F.261, A:V.379 Hydrogen bonds: A:L.94, A:D.95 pi-Stacking: A:Y.130

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

CL.2: 2 residues within 4Å: Chain A: K.53, R.55 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: R.35 Ligand excluded by PLIP

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

SO4.4: 6 residues within 4Å: Chain A: D.205, R.238, R.265, F.413, S.414, A.415 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:F.413, A:A.415 Water bridges: A:H.232, A:R.238, A:R.265, A:R.265, A:H.416 Salt bridges: A:R.238, A:R.265

2 x FE: FE (III) ION(Non-covalent)

FE.5: 6 residues within 4Å: Chain A: D.95, H.96, D.199, H.438 Ligands: XYX.1, FE.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.95, A:H.96, A:D.199, A:H.438 FE.6: 6 residues within 4Å: Chain A: H.91, H.93, H.178, D.199 Ligands: XYX.1, FE.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.91, A:H.93, A:H.178, A:D.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tao, Y. et al., Anticancer benzoxaboroles block pre-mRNA processing by directly inhibiting CPSF3. Cell Chem Biol (2024)

Release Date

2023-11-08

Peptides

Cleavage and polyadenylation specificity factor subunit 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cleavage and polyadenylation specificity factor subunit 3

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