SMTL ID : 7kdr.1

Crystal structure of Escherichia coli HPPK in complex with bisubstrate inhibitor HP-75

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

monomer

Ligands

1 x J1L: 5'-{[(2R,4R)-1-{2-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carbonyl)amino]ethyl}-2-carboxypiperidin-4-yl]sulfonyl}-5'-deoxyadenosine(Non-covalent)

J1L.1: 27 residues within 4Å: Chain A: G.8, T.42, P.43, P.44, L.45, P.47, Q.50, Y.53, N.55, L.70, Q.74, W.89, G.90, R.92, D.95, L.96, D.97, I.98, R.110, L.111, T.112, V.113, H.115, Y.116, R.121, F.123 Ligands: EDO.4 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:W.89 Hydrogen bonds: A:T.42, A:L.45, A:L.45, A:N.55, A:N.55, A:Q.74, A:I.98, A:R.110, A:T.112, A:T.112, A:H.115, A:Y.116 Water bridges: A:D.95, A:D.95, A:T.112, A:R.121, A:R.121 Salt bridges: A:D.95, A:D.97, A:H.115, A:R.121 pi-Stacking: A:Y.53, A:Y.53, A:F.123 pi-Cation interactions: A:Y.53, A:F.123

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

CL.2: 5 residues within 4Å: Chain A: P.114, K.119, F.137, P.138, D.139 Ligand excluded by PLIP

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

EDO.3: 3 residues within 4Å: Chain A: P.43, P.44, Q.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.48 Water bridges: A:D.52 EDO.4: 9 residues within 4Å: Chain A: A.6, I.7, G.8, N.55, D.95, D.97, F.123, M.124 Ligands: J1L.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.55 Water bridges: A:D.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, G. et al., Bisubstrate inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: Transition state analogs for high affinity binding. Bioorg.Med.Chem. (2021)

Release Date

2020-12-02

Peptides

2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase

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