SMTL ID : 8rib.2 (1 other biounit)

N-terminal domain of Trypanosoma brucei PEX14 in complex with a pyrazolo-pyrazolo[4,3-c]pyridin-3-yl compound showing a novel binding pose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.13 Å

Oligo State

monomer

Ligands

1 x OJN: 1-(2-azanylethyl)-5-[(4-methoxynaphthalen-1-yl)methyl]-~{N}-[(4-methylsulfanylphenyl)methyl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridine-3-carboxamide(Non-covalent)

OJN.1: 14 residues within 4Å: Chain A: K.12, R.13, N.16, A.17, F.20, R.25, V.26, T.29, S.33, K.34, F.37, L.38, K.41, L.43 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:N.16, A:R.25, A:V.26, A:K.41, A:L.43 Hydrogen bonds: A:N.16 Water bridges: A:N.16, A:N.16, A:N.16, A:K.41 pi-Stacking: A:F.20, A:F.37 pi-Cation interactions: A:K.41

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

EDO.2: 4 residues within 4Å: Chain A: T.60, N.62, E.63, R.66 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.60, A:T.60, A:E.63, A:R.66 EDO.3: 4 residues within 4Å: Chain A: K.39, A.45, L.68, S.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.39 Water bridges: A:A.45

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.4: 6 residues within 4Å: Chain A: H.36, R.66, I.67, L.68, S.69 Ligands: NA.5 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.36, A:R.66 Salt bridges: A:H.36

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

NA.5: 4 residues within 4Å: Chain A: K.65, R.66, L.68 Ligands: MLI.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.68 NA.6: 3 residues within 4Å: Chain A: S.8, E.9, R.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.8, A:E.9, A:R.10 NA.7: 3 residues within 4Å: Chain A: S.15, V.18, E.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.15, A:E.19 NA.8: 4 residues within 4Å: Chain A: T.31, F.52, Q.57, K.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.31, A:K.59

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

CL.9: 3 residues within 4Å: Chain A: P.30, T.31, S.32 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Menezes, F. et al., Quantum Chemistry in a Pocket. To Be Published

Release Date

2025-01-29

Peptides

Peroxisomal membrane protein PEX14: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Peroxisomal membrane protein PEX14

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