SMTL ID : 6jib.1

Human MTHFD2 in complex with DS44960156

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

4 x BQF: 4-(5-oxo-1,5-dihydro-2H-[1]benzopyrano[3,4-c]pyridine-3(4H)-carbonyl)benzoic acid(Non-covalent)

BQF.1: 12 residues within 4Å: Chain A: R.28, Y.69, N.72, K.73, Q.117, L.118, I.261, P.294, G.295, G.298, P.299, V.302 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.69, A:I.261, A:P.299, A:V.302 Hydrogen bonds: A:N.72, A:Q.117, A:G.295 Water bridges: A:K.73, A:G.296 Salt bridges: A:R.28, A:K.73 pi-Stacking: A:Y.69 BQF.3: 11 residues within 4Å: Chain A: A.184, G.185, S.216, H.217, R.218, T.220, K.222, L.225, A.239, I.241, L.244 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.218, A:K.222, A:A.239, A:I.241 BQF.7: 11 residues within 4Å: Chain B: Y.69, N.72, K.73, Q.117, L.118, I.261, P.294, G.295, G.298, P.299, V.302 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.69, B:I.261, B:V.302 Hydrogen bonds: B:N.72, B:Q.117, B:G.295 Water bridges: B:K.73, B:G.298 Salt bridges: B:K.73 pi-Stacking: B:Y.69 BQF.8: 11 residues within 4Å: Chain B: A.184, G.185, S.216, H.217, R.218, T.220, K.222, L.225, A.239, I.241, L.244 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:R.218, B:K.222, B:A.239, B:I.241, B:L.244 Hydrogen bonds: B:H.217

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

PO4.2: 4 residues within 4Å: Chain A: R.186, R.218 Chain B: D.201, H.204 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Water bridges: A:R.186, A:R.186, A:R.186, B:D.201 Salt bridges: A:R.186, A:R.218, B:H.204 Hydrogen bonds: B:D.201, B:D.201, B:D.201 PO4.6: 4 residues within 4Å: Chain A: D.201, H.204 Chain B: R.186, R.218 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Water bridges: B:R.186, B:R.218 Salt bridges: B:R.186, B:R.218, A:H.204

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: E.126, F.142, N.189 Ligands: GOL.5 6 PLIP interactions: 6 interactions with chain A Water bridges: A:E.126, A:S.187, A:K.188, A:K.188, A:N.189, A:N.189 GOL.5: 7 residues within 4Å: Chain A: E.126, R.127, F.142, K.188 Chain B: L.152 Ligands: GOL.4, GOL.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.126, A:E.126, A:R.127 GOL.9: 7 residues within 4Å: Chain A: R.127 Chain B: L.152, D.153, Q.154, H.204, E.205 Ligands: GOL.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.205 GOL.10: 5 residues within 4Å: Chain B: E.126, F.142, S.187, N.189 Ligands: GOL.11 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.188, B:K.188 GOL.11: 6 residues within 4Å: Chain A: L.152 Chain B: E.126, R.127, F.142, K.188 Ligands: GOL.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.126, B:R.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawai, J. et al., Structure-Based Design and Synthesis of an Isozyme-Selective MTHFD2 Inhibitor with a Tricyclic Coumarin Scaffold. Acs Med.Chem.Lett. (2019)

Release Date

2019-06-05

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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