SMTL ID : 8coq.1

Mycobacterium tuberculosis dihydrofolate reductase in complex with 5-(cyclopropylethynyl)-6-(2-methoxyphenyl)pyrimidine-2,4-diamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 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: VDT.2 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:T.48 Hydrogen bonds: A:A.9, A:R.18, A:G.20, A:G.20, A:G.45, A:G.45, A:R.46, A:R.46, A:R.47, A:R.47, A:T.48, A:S.68, A:R.69, A:R.69, A:R.69, A:G.98, A:G.99, A:Q.100, A:V.101, A:Y.102, A:Y.102 Water bridges: A:G.17, A:R.18, A:S.51 Salt bridges: A:R.46, A:R.47 pi-Cation interactions: A:R.69, A:R.69 NDP.5: 26 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, I.96, G.97, G.98, G.99, Q.100, V.101, Y.102, L.104, A.128 Ligands: VDT.6 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:T.48 Hydrogen bonds: B:A.9, B:R.18, B:G.20, B:G.20, B:G.45, B:R.46, B:R.46, B:R.47, B:R.47, B:T.48, B:S.68, B:R.69, B:R.69, B:Q.70, B:Q.70, B:G.97, B:G.98, B:G.99, B:Q.100, B:V.101, B:Y.102, B:Y.102 Water bridges: B:R.69, B:R.69, B:R.69 Salt bridges: B:R.46 pi-Cation interactions: B:R.69

2 x VDT: 5-(2-cyclopropylethynyl)-6-(2-methoxyphenyl)pyrimidine-2,4-diamine(Non-covalent)

VDT.2: 14 residues within 4Å: Chain A: I.7, W.8, A.9, I.22, W.24, D.29, Q.30, F.33, T.48, L.52, I.96, Y.102, T.115 Ligands: NDP.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Q.30, A:F.33, A:F.33, A:F.33, A:T.48, A:L.52 Hydrogen bonds: A:I.7, A:W.8, A:T.115 Water bridges: A:D.29, A:T.115 Salt bridges: A:D.29 VDT.6: 13 residues within 4Å: Chain B: I.7, W.8, A.9, I.22, D.29, Q.30, F.33, T.48, L.52, I.96, Y.102, T.115 Ligands: NDP.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Q.30, B:F.33, B:F.33, B:T.48, B:L.52, B:L.52, B:I.96 Hydrogen bonds: B:I.7, B:T.115, B:T.115 Salt bridges: B:D.29 pi-Stacking: B:F.33

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

CO.3: 4 residues within 4Å: Chain A: I.36, H.40, E.92 Chain B: H.159 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: A:H.40, B:H.159, H2O.1, H2O.2, H2O.2, H2O.3 CO.7: 4 residues within 4Å: Chain A: H.159 Chain B: I.36, H.40, E.92 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.40, H2O.4, H2O.4, H2O.4, H2O.5

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

SO4.4: 3 residues within 4Å: Chain A: F.33, R.34, R.62 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.34, A:R.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirkman, T.J. et al., Currently unpublished. To Be Published

Release Date

2024-03-06

Peptides

Dihydrofolate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase

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