SMTL ID : 4isk.1 (3 other biounits)

Crystal structure of E.coli thymidylate synthase with dUMP and the BGC 945 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

1 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.1: 16 residues within 4Å: Chain A: R.21, Y.94, L.143, C.146, H.147, Q.165, R.166, S.167, C.168, D.169, G.173, N.177, H.207, Y.209 Chain B: R.126 Ligands: 1JY.3 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:D.169 Hydrogen bonds: A:Q.165, A:S.167, A:D.169, A:N.177, A:N.177, A:H.207 Water bridges: A:H.147, A:H.147, A:R.166, A:R.166, B:R.126, B:R.126 Salt bridges: A:R.21, A:R.166, B:R.126

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: I.79 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: T.78, I.79 Ligands: 1JY.6 No protein-ligand interaction detected (PLIP)

2 x 1JY: N-(4-{[(6S)-2-(hydroxymethyl)-4-oxo-4,6,7,8-tetrahydro-1H-cyclopenta[g]quinazolin-6-yl](prop-2-yn-1-yl)amino}benzoyl)-L-gamma-glutamyl-D-glutamic acid(Non-covalent)

1JY.3: 20 residues within 4Å: Chain A: T.22, K.48, H.51, S.54, E.58, T.78, I.79, W.80, W.83, L.143, D.169, L.172, G.173, F.176, N.177, Y.209, H.212, V.262, A.263 Ligands: UMP.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.79, A:I.79, A:W.80, A:W.80, A:W.83, A:W.83, A:L.143, A:F.176 Hydrogen bonds: A:Y.209, A:A.263 Water bridges: A:K.48, A:K.48, A:H.51, A:T.78, A:T.78, A:I.79, A:V.262, A:A.263 Salt bridges: A:K.48, A:H.51 pi-Stacking: A:F.176 1JY.6: 21 residues within 4Å: Chain B: K.48, H.51, R.53, S.54, E.58, T.78, I.79, W.80, W.83, L.143, D.169, L.172, G.173, F.176, N.177, Y.209, H.212, V.262, A.263 Ligands: UMC.4, MG.5 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:I.79, B:I.79, B:W.80, B:W.80, B:W.83, B:W.83, B:L.143, B:F.176, B:F.176, B:F.176 Hydrogen bonds: B:H.51, B:S.54, B:T.78, B:D.169, B:A.263, B:A.263 Water bridges: B:K.48, B:K.48, B:T.78, B:T.78, B:I.258 Salt bridges: B:K.48, B:H.51

1 x UMC: 2'-deoxy-5'-uridylic acid(Non-covalent)

UMC.4: 17 residues within 4Å: Chain A: R.126 Chain B: R.21, Y.94, L.143, A.144, C.146, H.147, Q.165, R.166, S.167, C.168, D.169, G.173, N.177, H.207, Y.209 Ligands: 1JY.6 14 PLIP interactions: 3 interactions with chain A, 11 interactions with chain B Water bridges: A:R.126, A:R.126, B:H.147, B:R.166 Salt bridges: A:R.126, B:R.21, B:R.166 Hydrogen bonds: B:Q.165, B:S.167, B:S.167, B:D.169, B:N.177, B:N.177, B:H.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tochowicz, A. et al., Development and Binding Mode Assessment of N-[4-[2-Propyn-1-yl[(6S)-4,6,7,8-tetrahydro-2-(hydroxymethyl)-4-oxo-3H-cyclopenta[g]quinazolin-6-yl]amino]benzoyl]-l-gamma-glutamyl-d-glutamic Acid (BGC 945), a Novel Thymidylate Synthase Inhibitor That Targets Tumor Cells. J.Med.Chem. (2013)

Release Date

2013-12-25

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

Thymidylate synthase

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