SMTL ID : 6vs9.3 (2 other biounits)

Mycobacterium tuberculosis dihydrofolate reductase in complex with 3-(piperidin-1-ylmethyl)benzoic acid(fragment 11)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

2 x RK4: 3-[(piperidin-1-yl)methyl]benzoic acid(Non-covalent)

RK4.1: 7 residues within 4Å: Chain A: Q.30, F.33, R.34, V.56, R.62 Ligands: NAP.2, GOL.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.33, A:F.33, A:V.56 Salt bridges: A:R.62 RK4.9: 7 residues within 4Å: Chain B: F.33, R.34, L.52, V.56, L.59, R.62 Ligands: NAP.10 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.33, B:L.52, B:V.56, B:L.59 Salt bridges: B:R.34, B:R.62 pi-Cation interactions: B:F.33

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 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: RK4.1 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:I.22, A:T.48 Hydrogen bonds: A:A.9, 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:R.47, A:T.48, A:R.69, A:Q.70, A:Q.70, A:G.98, A:G.99, A:Q.100, A:V.101, A:Y.102, A:Y.102 Water bridges: A:S.51, A:R.69, A:L.84 Salt bridges: A:R.46, A:R.69 pi-Cation interactions: A:R.69 NAP.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: RK4.9 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:I.22, B:T.48 Hydrogen bonds: B:A.9, 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: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, B:Y.102, B:Y.102 Water bridges: B:G.17, B:R.18, B:R.47, B:S.51, B:R.69 Salt bridges: B:R.46, B:R.47 pi-Cation interactions: B:R.69, B:R.69

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

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

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

PO4.5: 3 residues within 4Å: Chain A: R.34, M.38, P.60 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.34 PO4.6: 2 residues within 4Å: Chain A: R.46, R.47 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.46, A:D.50 Salt bridges: A:R.46, A:R.47 PO4.11: 2 residues within 4Å: Chain B: R.46, R.47 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.46 Salt bridges: B:R.46, B:R.47

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: A.9, W.24, R.25, L.26, D.29, Q.30 Ligands: RK4.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.26, A:D.29, A:Q.30

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

SO4.8: 4 residues within 4Å: Chain A: E.28, A.31, R.148 Chain B: R.138 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:R.138 Salt bridges: B:R.138, A:R.148

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