SMTL ID : 7ehj.1

human MTHFD2 in complex with compound 21, cofactor and phosphate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-dimer

Ligands

2 x J49: (2S)-2-[[4-[(4-azanyl-6-oxidanyl-pyrimidin-5-yl)carbamoylamino]phenyl]carbonylamino]pentanedioic acid(Non-covalent)

J49.1: 18 residues within 4Å: Chain A: S.48, Y.49, N.52, K.53, V.96, Q.97, L.98, D.120, F.122, I.241, L.254, P.274, G.275, G.278, P.279, T.281, V.282 Ligands: NAD.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.49, A:I.241, A:T.281, A:V.282 Hydrogen bonds: A:S.48, A:N.52, A:K.53, A:Q.97, A:L.98, A:L.98, A:G.275, A:G.278 Water bridges: A:D.120, A:A.140, A:T.141, A:G.276 pi-Stacking: A:Y.49 pi-Cation interactions: A:K.53 J49.5: 19 residues within 4Å: Chain B: R.8, S.48, Y.49, N.52, K.53, V.96, Q.97, L.98, D.120, F.122, I.241, L.254, P.274, G.275, G.278, P.279, T.281, V.282 Ligands: NAD.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.49, B:I.241, B:T.281, B:V.282 Hydrogen bonds: B:S.48, B:N.52, B:K.53, B:Q.97, B:L.98, B:L.98, B:G.275 Water bridges: B:A.140, B:G.278, B:G.278 Salt bridges: B:R.8 pi-Stacking: B:Y.49 pi-Cation interactions: B:K.53

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 22 residues within 4Å: Chain A: T.141, A.164, G.165, R.166, S.167, V.170, H.197, R.198, A.218, A.219, G.220, I.221, L.224, V.239, G.240, I.241, N.242, V.277, G.278, T.281 Ligands: J49.1, PO4.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.166, A:S.167, A:S.167, A:S.167, A:R.198, A:R.198, A:R.198, A:I.241, A:N.242, A:V.277 Water bridges: A:T.200, A:V.277 NAD.6: 20 residues within 4Å: Chain B: T.141, G.165, R.166, S.167, H.197, R.198, A.218, A.219, G.220, I.221, L.224, V.239, G.240, I.241, N.242, V.277, G.278, T.281 Ligands: PO4.4, J49.5 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.141 Hydrogen bonds: B:R.166, B:S.167, B:S.167, B:R.198, B:R.198, B:R.198, B:I.241, B:N.242, B:V.277, B:T.281 Water bridges: B:S.167, B:S.167

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

PO4.3: 5 residues within 4Å: Chain A: R.166, R.198 Chain B: D.181, H.184 Ligands: NAD.2 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:H.184, A:R.166, A:R.198 Water bridges: A:R.166, A:R.198 PO4.4: 5 residues within 4Å: Chain A: D.181, H.184 Chain B: R.166, R.198 Ligands: NAD.6 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.181, A:D.181, A:D.181 Water bridges: A:D.181, B:R.166 Salt bridges: A:H.184, B:R.166, B:R.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, L.C. et al., Xanthine Derivatives Reveal an Allosteric Binding Site in Methylenetetrahydrofolate Dehydrogenase 2 (MTHFD2). J.Med.Chem. (2021)

Release Date

2021-08-11

Peptides

Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial

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