SMTL ID : 8cq8.1

Mycobacterium tuberculosis dihydrofolate reductase in complex with methyl 4-(2,6-diamino-5-(cyclopropylethynyl)pyrimidin-4-yl)benzoate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x VFF: methyl 4-[2,6-bis(azanyl)-5-(2-cyclopropylethynyl)pyrimidin-4-yl]benzoate(Non-covalent)

VFF.1: 15 residues within 4Å: Chain A: I.7, W.8, A.9, I.22, R.25, D.29, Q.30, F.33, T.48, L.52, I.96, Y.102, T.115 Ligands: MES.2, NDP.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.22, A:Q.30, A:F.33, A:T.48, A:L.52, A:I.96 Hydrogen bonds: A:I.7, A:W.8, A:Y.102, A:T.115 Water bridges: A:R.25, A:R.25, A:T.115 Salt bridges: A:R.25, A:D.29 pi-Stacking: A:F.33 VFF.7: 16 residues within 4Å: Chain B: I.7, W.8, A.9, I.22, R.25, D.29, Q.30, F.33, T.48, L.52, I.96, Y.102, T.115 Ligands: MES.8, MES.9, NDP.10 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.22, B:Q.30, B:F.33, B:F.33, B:F.33, B:T.48, B:L.52, B:I.96 Hydrogen bonds: B:Y.102, B:Y.102, B:T.115, B:T.115 Salt bridges: B:D.29 pi-Stacking: B:F.33

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 7 residues within 4Å: Chain A: Q.30, F.33, R.34, L.52, V.56, R.62 Ligands: VFF.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.30 Salt bridges: A:R.34, A:R.62 MES.8: 9 residues within 4Å: Chain B: Q.30, F.33, R.34, L.52, V.56, L.59, R.62 Ligands: VFF.7, MES.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.30 Salt bridges: B:R.62 MES.9: 7 residues within 4Å: Chain B: D.21, R.25, S.51, P.53, V.56 Ligands: VFF.7, MES.8 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:D.21, B:R.25

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

NDP.3: 27 residues within 4Å: Chain A: W.8, A.9, I.16, G.17, R.18, G.20, D.21, I.22, G.45, R.46, R.47, T.48, L.67, S.68, R.69, Q.70, G.82, I.96, G.97, G.98, G.99, Q.100, V.101, Y.102, L.104, A.128 Ligands: VFF.1 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:T.48 Hydrogen bonds: A:A.9, A:I.16, A:R.18, A:G.20, A:R.46, A:R.46, A:R.47, A:R.47, A:T.48, A:T.48, A:S.68, A:R.69, A:R.69, A:Q.70, A:G.98, A:G.99, A:Q.100, A:V.101 Water bridges: A:G.20, A:S.51 Salt bridges: A:R.46, A:R.47 pi-Cation interactions: A:R.69 NDP.10: 27 residues within 4Å: Chain B: W.8, A.9, I.16, G.17, R.18, G.20, D.21, I.22, G.45, R.46, R.47, T.48, L.67, S.68, R.69, Q.70, G.82, I.96, G.97, G.98, G.99, Q.100, V.101, Y.102, L.104, A.128 Ligands: VFF.7 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:I.22, B:T.48 Hydrogen bonds: B:A.9, B:I.16, B:R.18, B:G.20, B:G.20, B:R.46, B:R.46, B:R.47, B:R.47, B:T.48, B:T.48, B:S.68, B:R.69, B:R.69, B:Q.70, B:Q.70, B:G.98, B:G.99, B:Q.100, B:V.101 Water bridges: B:S.51 Salt bridges: B:R.46, B:R.47

2 x CO: COBALT (II) ION(Non-covalent)

CO.4: 4 residues within 4Å: Chain A: H.40, E.92 Chain B: T.110, H.159 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:H.159, A:H.40, H2O.2, H2O.2, H2O.4 CO.11: 3 residues within 4Å: Chain A: H.159 Chain B: I.36, H.40 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.40, H2O.3, H2O.4, H2O.4

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

SO4.5: 2 residues within 4Å: Chain A: R.46, R.47 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.46, A:R.47 SO4.6: 2 residues within 4Å: Chain A: R.25, P.53 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.25 SO4.12: 2 residues within 4Å: Chain B: R.46, R.47 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.46, B:R.46, B:R.47 Salt bridges: B:R.46, B:R.47 SO4.13: 2 residues within 4Å: Chain B: A.31, R.148 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirkman, T.J. et al., Expansion of a series of pyrimidine derivatives utilising fragment-based merging leads to increased affinity to Mycobacterium tuberculosis dihydrofolate reductase (unpublished currently). To Be Published

Release Date

2024-03-13

Peptides

Dihydrofolate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase

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