SMTL ID : 5v7i.1

Crystal structure of homo sapiens serine hydroxymethyltransferase 2 (mitochondrial) (SHMT2), in complex with glycine, PLP and folate-competitive pyrazolopyran inhibitor: 6-amino-4-isopropyl-3-methyl-4-(3-(pyrrolidin-1-yl)-5-(trifluoromethyl)phenyl)-1,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

homo-dimer

Ligands

2 x 8Z1: (4R)-6-amino-3-methyl-4-(propan-2-yl)-4-[3-(pyrrolidin-1-yl)-5-(trifluoromethyl)phenyl]-1,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile(Non-covalent)

8Z1.1: 12 residues within 4Å: Chain A: L.138, G.141, G.142, H.143, L.144, S.198, K.381, N.382, R.397 Chain B: E.70, Y.77, Y.78 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.138, A:L.138, A:L.144, B:Y.77, B:Y.78 Hydrogen bonds: A:G.142, A:H.143, A:L.144, A:S.198 pi-Stacking: B:Y.77 8Z1.5: 11 residues within 4Å: Chain A: E.70, Y.77, Y.78 Chain B: L.138, G.142, H.143, L.144, S.198, K.381, R.397 Ligands: GLY.7 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.77, A:Y.77, A:Y.77, B:L.138 Hydrogen bonds: B:G.142, B:H.143, B:L.144, B:S.198, B:N.382

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: K.172, T.173, G.174, V.345, S.346, G.347 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.172, A:S.346, A:S.346 GOL.6: 6 residues within 4Å: Chain B: R.359, D.387, R.388, S.389, T.392, G.394 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.388, B:S.389, B:S.389 Water bridges: B:D.357, B:D.364, B:D.387

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 7 residues within 4Å: Chain A: F.99, D.100, Q.105, W.106, F.240, K.241, R.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.105 Water bridges: A:S.238 PEG.4: 4 residues within 4Å: Chain A: M.149, V.152, K.153, R.154 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.154

1 x GLY: GLYCINE(Non-covalent)

GLY.7: 10 residues within 4Å: Chain A: Y.68, E.70, Y.78 Chain B: S.48, H.143, S.198, H.226, K.252, R.397 Ligands: 8Z1.5 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.70, A:Y.78 Water bridges: A:Y.68 Salt bridges: B:H.226, B:R.397

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ducker, G.S. et al., Human SHMT inhibitors reveal defective glycine import as a targetable metabolic vulnerability of diffuse large B-cell lymphoma. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-10-11

Peptides

Serine hydroxymethyltransferase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine hydroxymethyltransferase, mitochondrial

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