SMTL ID : 3ghc.1

Design, Synthesis, and X-ray Crystal Structure of Classical and Nonclassical 2-amino-4-oxo-5-substituted-6-thieno[2,3-d]pyrimidines as dual thymidylate synthase and dihydrofolate reductase inhibitors and as potential antitumor agenst

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x GHC: N-({4-[(2-amino-6-ethyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-5-yl)sulfanyl]phenyl}carbonyl)-L-glutamic acid(Non-covalent)

GHC.1: 18 residues within 4Å: Chain A: I.7, V.8, A.9, L.22, E.30, F.31, R.32, F.34, S.35, T.56, I.60, S.64, L.67, R.70, V.115, Y.121, T.136 Ligands: NDP.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.31, A:F.34, A:T.56, A:V.115 Hydrogen bonds: A:S.35, A:S.64, A:T.136, A:T.136 Water bridges: A:E.30, A:E.30, A:K.68, A:R.70, A:R.70 Salt bridges: A:E.30, A:K.68, A:R.70 pi-Stacking: A:F.34

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 28 residues within 4Å: Chain A: V.8, A.9, I.16, G.17, K.18, G.20, D.21, L.22, W.24, G.53, K.54, K.55, T.56, S.59, L.75, S.76, R.77, E.78, R.91, S.92, V.115, G.117, S.118, V.120, Y.121, E.123, T.146 Ligands: GHC.1 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:T.56 Hydrogen bonds: A:A.9, A:I.16, A:K.18, A:G.20, A:G.20, A:G.53, A:K.54, A:K.55, A:T.56, A:S.59, A:S.76, A:R.77, A:E.78, A:L.93, A:G.117, A:S.118, A:E.123 Water bridges: A:K.55, A:R.77, A:G.117, A:S.118, A:S.118, A:S.119, A:S.119, A:S.119, A:S.119, A:S.119, A:E.123, A:T.146 Salt bridges: A:K.54

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

SO4.3: 9 residues within 4Å: Chain A: L.158, L.159, P.160, E.161, Y.162, V.165, F.179, E.180, V.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.159, A:V.181 Water bridges: A:Y.162 SO4.4: 3 residues within 4Å: Chain A: K.122, P.149, E.150 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.150 Water bridges: A:E.150, A:E.150, A:E.150, A:E.150 Salt bridges: A:K.122 SO4.5: 1 residues within 4Å: Chain A: K.157 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.157 Salt bridges: A:K.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gangjee, A. et al., Design, synthesis, and X-ray crystal structure of classical and nonclassical 2-amino-4-oxo-5-substituted-6-ethylthieno[2,3-d]pyrimidines as dual thymidylate synthase and dihydrofolate reductase inhibitors and as potential antitumor agents. J.Med.Chem. (2009)

Release Date

2009-09-22

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydrofolate reductase