SMTL ID : 7ehm.1

Human MTHFD2 in complex with compound 21 and 15

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

2 x J4C: (2S)-2-[[4-[[1-[(3,4-dichlorophenyl)methyl]-3,7-dimethyl-2,6-bis(oxidanylidene)purin-8-yl]amino]phenyl]carbonylamino]pentanedioic acid(Non-covalent)

J4C.1: 18 residues within 4Å: Chain A: Y.49, L.98, P.99, E.106, R.107, G.121, F.122, V.127, M.130, P.139, K.168, N.169, M.172, P.173, M.176 Chain B: C.131, L.132 Ligands: J49.2 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.127, A:V.127, A:P.173, B:L.132 Hydrogen bonds: A:E.106, A:R.107, A:N.169 pi-Stacking: A:F.122, A:F.122 J4C.3: 18 residues within 4Å: Chain A: C.131, M.176 Chain B: Y.49, L.98, P.99, E.106, R.107, G.121, F.122, V.127, M.130, P.139, N.169, M.172, P.173, M.176, I.241 Ligands: J49.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.98, B:V.127, B:V.127, B:P.173, B:I.241 Hydrogen bonds: B:E.106, B:R.107, B:N.169 Water bridges: B:Y.49, B:Q.97 pi-Stacking: B:F.122, B:F.122

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

J49.2: 17 residues within 4Å: Chain A: S.48, Y.49, N.52, K.53, V.96, Q.97, L.98, D.120, F.122, R.243, L.254, P.274, G.275, G.278, P.279, V.282 Ligands: J4C.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.49, A:L.254, 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:S.48, A:T.141, A:T.141, A:G.276, A:G.276 Salt bridges: A:R.243 pi-Stacking: A:Y.49 pi-Cation interactions: A:K.53 J49.4: 19 residues within 4Å: Chain B: S.48, Y.49, N.52, K.53, V.96, Q.97, L.98, D.120, F.122, I.241, R.243, L.254, P.274, G.275, G.278, P.279, T.281, V.282 Ligands: J4C.3 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:Y.49, B:I.241, B:L.254, 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, B:G.278 Water bridges: B:R.8, B:Y.49, B:T.141, B:T.141, B:R.243, B:G.276 Salt bridges: B:R.243 pi-Stacking: B:Y.49 pi-Cation interactions: B:K.53

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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