SMTL ID : 3ntz.1

Design, Synthesis, Biological Evaluation and X-ray Crystal Structures of Novel Classical 6,5,6-tricyclicbenzo[4,5]thieno[2,3-d]pyrimidines as Dual Thymidylate Synthase and Dihydrofolate Reductase Inhibitors

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

1 x 3TZ: N-[(4-{[(2-amino-4-oxo-3,4-dihydro[1]benzothieno[2,3-d]pyrimidin-5-yl)methyl]amino}phenyl)carbonyl]-L-glutamic acid(Non-covalent)

3TZ.1: 17 residues within 4Å: Chain A: I.7, V.8, A.9, L.22, E.30, F.31, R.32, F.34, Q.35, T.56, N.64, L.67, R.70, V.115, Y.121, T.136 Ligands: NDP.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.31, A:F.31, A:F.34, A:F.34, A:Q.35, A:T.56, A:V.115 Hydrogen bonds: A:Q.35, A:T.136, A:T.136 Water bridges: A:E.30, A:E.30, A:R.32, A:K.68 Salt bridges: A:E.30, A:R.70

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, S.119, Y.121, E.123, T.146 Ligands: 3TZ.1 27 PLIP interactions: 27 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: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.54, A:K.54, A:G.117, A:S.118, A:S.118, A:S.119, A:S.119, A:S.119, A:E.123 Salt bridges: A:K.54

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

SO4.3: 2 residues within 4Å: Chain A: R.77, R.91 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.77, A:R.91 SO4.4: 2 residues within 4Å: Chain A: E.172, K.173 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.173 Water bridges: A:G.174 SO4.5: 2 residues within 4Å: Chain A: E.62, R.65 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.62, A:R.65 Water bridges: A:F.58, A:I.60 SO4.6: 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:V.181 Water bridges: A:Y.162, A:Y.162 SO4.7: 3 residues within 4Å: Chain A: K.122, P.149, E.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.150 Salt bridges: A:K.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Design, synthesis, biological evaluation and X-ray crystal structure of novel classical 6,5,6-tricyclic benzo[4,5]thieno[2,3-d]pyrimidines as dual thymidylate synthase and dihydrofolate reductase inhibitors. Bioorg.Med.Chem. (2011)

Release Date

2011-05-25

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydrofolate reductase

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