SMTL ID : 6vs5.3 (2 other biounits)

Mycobacterium tuberculosis dihydrofolate reductase in complex with 5-methyl-1-phenyl-1H-pyrazole-4-carboxylic acid (fragment 1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

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

CO.1: 4 residues within 4Å: Chain A: I.36, H.40, E.92 Chain B: H.159 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: B:H.159, A:H.40, H2O.1, H2O.1, H2O.2, H2O.4 CO.7: 4 residues within 4Å: Chain A: H.159 Chain B: I.36, H.40, E.92 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: A:H.159, B:H.40, H2O.8, H2O.8, H2O.9, H2O.9

4 x 9FH: 5-methyl-1-phenyl-pyrazole-4-carboxylic acid(Non-covalent)

9FH.2: 9 residues within 4Å: Chain A: I.22, R.25, L.26, D.29, Q.30, F.33, L.52 Ligands: 9FH.3, NDP.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.22, A:Q.30, A:L.52 Hydrogen bonds: A:L.26, A:Q.30 Water bridges: A:D.29 pi-Stacking: A:F.33 9FH.3: 10 residues within 4Å: Chain A: R.25, Q.30, F.33, R.34, L.52, P.53, V.56, L.59, R.62 Ligands: 9FH.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.33, A:L.52, A:L.59 Water bridges: A:R.34 Salt bridges: A:R.62 9FH.8: 8 residues within 4Å: Chain B: I.22, R.25, L.26, D.29, Q.30, F.33 Ligands: 9FH.9, NDP.10 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.22, B:Q.30 Hydrogen bonds: B:L.26, B:Q.30 Water bridges: B:W.24 Salt bridges: B:R.25 pi-Stacking: B:F.33 9FH.9: 8 residues within 4Å: Chain B: Q.30, F.33, R.34, P.53, V.56, L.59, R.62 Ligands: 9FH.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.33, B:L.59 Salt bridges: B:R.62

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

NDP.4: 28 residues within 4Å: Chain A: W.8, A.9, I.16, G.17, R.18, G.20, D.21, I.22, W.24, 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: 9FH.2 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:I.22, A:T.48 Hydrogen bonds: A:A.9, A:I.16, A:R.18, A:G.20, A:G.20, A:G.45, A:R.46, A:R.46, A:R.47, A:R.47, A:T.48, A:T.48, A:R.69, A:R.69, A:R.69, A:Q.70, A:Q.70, A:G.98, A:G.99, A:Q.100, A:Q.100, A:V.101 Water bridges: A:G.17, A:S.51 Salt bridges: A:R.46, A:R.47 pi-Cation interactions: A:R.69, 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: 9FH.8 32 PLIP interactions: 32 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:R.69, B:Q.70, B:G.97, B:G.98, B:G.99, B:Q.100, B:V.101 Water bridges: B:R.47, B:R.47, B:S.51, B:R.69, B:Q.100 Salt bridges: B:R.46, B:R.47 pi-Cation interactions: B:R.69, B:R.69

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 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 PO4.6: 2 residues within 4Å: Chain A: R.25, P.53 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.25, A:R.25 Salt bridges: A:R.25 PO4.11: 2 residues within 4Å: Chain B: R.46, R.47 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.46, B:R.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ribeiro, J.A. et al., Using a Fragment-Based Approach to Identify Alternative Chemical Scaffolds Targeting Dihydrofolate Reductase fromMycobacterium tuberculosis. Acs Infect Dis. (2020)

Release Date

2020-07-15

Peptides

Dihydrofolate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrofolate reductase

Related Entries With Identical Sequence