SMTL ID : 8cop.1

Mycobacterium tuberculosis dihydrofolate reductase in complex with N-(4-(2,6-diamino-5-(cyclopropylethynyl)pyrimidin-4-yl)phenyl)methanesulfonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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, 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 Ligands: VCI.4 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:A.9, A:R.18, A:D.21, A:R.46, A:R.47, A:R.47, A:R.47, A:T.48, A:T.48, A:R.69, A:R.69, A:Q.70, A:G.97, A:G.98, A:G.99, A:Q.100, A:V.101, A:Y.102 Water bridges: A:G.17, A:G.20, A:S.51 Salt bridges: A:R.46, A:R.47 pi-Cation interactions: A:R.69, A:R.69 NDP.6: 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: VCI.8 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.22, B:T.48 Hydrogen bonds: B:A.9, B:R.18, B:G.20, B:R.46, B:R.47, B:R.47, B:T.48, B:T.48, B:S.68, B:R.69, B:G.98, B:G.99, B:Q.100, B:V.101, B:Y.102 Salt bridges: B:R.46

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

PO4.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PO4.3: 1 residues within 4Å: Chain A: K.55 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.55 PO4.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x VCI: ~{N}-[4-[2,6-bis(azanyl)-5-(2-cyclopropylethynyl)pyrimidin-4-yl]phenyl]methanesulfonamide(Non-covalent)

VCI.4: 14 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: NDP.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.22, A:T.48, A:L.52 Hydrogen bonds: A:R.25, A:Q.30, A:Y.102, A:Y.102, A:T.115, A:T.115 Water bridges: A:T.115 Salt bridges: A:D.29 pi-Stacking: A:F.33 VCI.8: 15 residues within 4Å: Chain B: I.7, W.8, A.9, I.22, W.24, R.25, L.26, D.29, Q.30, F.33, T.48, I.96, Y.102, T.115 Ligands: NDP.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.22, B:Q.30, B:F.33, B:T.48, B:I.96 Hydrogen bonds: B:W.8, B:L.26, B:Y.102, B:Y.102, B:T.115 Salt bridges: B:D.29 pi-Stacking: B:F.33

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

CO.5: 4 residues within 4Å: Chain A: I.36, H.40, E.92 Chain B: H.159 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.159, A:H.40, H2O.1, H2O.1 CO.9: 5 residues within 4Å: Chain A: H.159, S.161 Chain B: I.36, H.40, E.92 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.159, B:H.40, H2O.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirkmna, T.J. et al., Expansion of a series of pyrimidine derivatives utilising fragment-based merging showcasing anleads to increased affinity with to Mycobacterium tuberculosis dihydrofolate reductase. 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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