SMTL ID : 7dyu.1

Human JMJD5 in complex with MN and 5-((4-phenylbutyl)amino)pyridine-2,4-dicarboxylic acid.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 2 residues within 4Å: Chain A: R.87, D.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.87 TRS.3: 7 residues within 4Å: Chain A: L.19, V.20, P.21, G.22, Q.145, P.214, V.215 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.145

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: H.140, D.142, H.219, W.233 Ligands: HR9.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.140, A:D.142, A:H.219, H2O.2

1 x HR9: 5-(4-phenylbutylamino)pyridine-2,4-dicarboxylic acid(Non-covalent)

HR9.4: 22 residues within 4Å: Chain A: E.57, V.58, G.59, W.67, V.89, Y.91, A.93, W.129, T.135, I.136, S.137, P.138, H.140, D.142, N.146, L.148, K.155, H.219, V.221, S.231, W.233 Ligands: MN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.57, A:V.89, A:Y.91, A:Y.91, A:W.129 Hydrogen bonds: A:Y.91, A:N.146, A:W.233 Salt bridges: A:K.155, A:H.219 pi-Stacking: A:Y.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brewitz, L. et al., 5-Substituted Pyridine-2,4-dicarboxylate Derivatives Have Potential for Selective Inhibition of Human Jumonji-C Domain-Containing Protein 5. J.Med.Chem. (2023)

Release Date

2022-02-02

Peptides

Bifunctional peptidase and arginyl-hydroxylase JMJD5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bifunctional peptidase and arginyl-hydroxylase JMJD5

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