SMTL ID : 4m5k.1

The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.1: 20 residues within 4Å: Chain A: L.74, Q.78, R.86, R.88, W.93, R.96, D.99, L.100, D.101, I.102, R.114, L.115, T.116, V.117, H.119, Y.120, R.125 Ligands: CA.2, CA.3, GOL.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.78, A:R.86, A:R.86, A:R.88, A:R.88, A:R.96, A:R.96, A:I.102, A:T.116, A:T.116 Water bridges: A:D.99 Salt bridges: A:H.119, A:R.125

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.99, D.101 Ligands: APC.1, CA.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.99, A:D.101, H2O.2, H2O.2 CA.3: 4 residues within 4Å: Chain A: D.99, D.101 Ligands: APC.1, CA.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.99, A:D.101, H2O.1, H2O.1 CA.4: 3 residues within 4Å: Chain A: G.30, I.32, S.35 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.30, A:I.32, A:S.35, H2O.2, H2O.2

1 x YH3: 2-amino-8-{[2-(3-methylphenyl)-2-oxoethyl]sulfanyl}-1,9-dihydro-6H-purin-6-one(Non-covalent)

YH3.5: 11 residues within 4Å: Chain A: T.46, P.47, P.48, L.49, G.50, Y.57, N.59, W.93, D.121, R.125, F.127 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.49, A:L.49, A:W.93 Hydrogen bonds: A:T.46, A:T.46, A:L.49, A:L.49, A:N.59, A:N.59 pi-Stacking: A:Y.57, A:Y.57, A:F.127 pi-Cation interactions: A:F.127

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: H.119, Y.120 Ligands: APC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yun, M.K. et al., The identification, analysis and structure-based development of novel inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Bioorg.Med.Chem. (2014)

Release Date

2014-04-02

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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