SMTL ID : 6bm7.2 (1 other biounit)

Crystal structure of Trypanosoma brucei AdoMetDC/prozyme heterodimer in complex with pyrimidineamine inhibitor UTSAM568

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.98 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.1: 19 residues within 4Å: Chain A: R.34, E.36, I.38 Chain B: R.9, E.39, W.40, V.96, S.100, C.101, S.102, D.103, D.104, A.105, Q.106, F.219, I.220, D.221, Y.256, H.260 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.9, B:E.39, B:S.100, B:D.104, B:F.219, B:D.221, B:Y.256, A:E.36

1 x DY7: 2-amino-4-[(3,5-dibromophenyl)amino]-6-methylpyrimidin-1-ium(Non-covalent)

DY7.2: 15 residues within 4Å: Chain A: F.28, S.84, E.85 Chain B: X.1, C.15, Y.158, P.160, C.161, G.162, S.164, H.177, I.178, T.179, P.180, E.181 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.179 Salt bridges: B:E.181 pi-Stacking: B:Y.158, A:F.28 Hydrophobic interactions: A:F.28 pi-Cation interactions: A:F.28

1 x PUT: 1,4-DIAMINOBUTANE(Non-covalent)

PUT.3: 14 residues within 4Å: Chain C: E.42, N.44, Q.95, W.126, I.183, R.191, E.193, D.195, Q.197, L.280, D.282, R.283, Y.314, F.316 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.126 Hydrogen bonds: C:E.42, C:D.195, C:D.282

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 8 residues within 4Å: Chain C: I.123, V.124, D.125, Y.180, G.182, I.183, D.184, R.185 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.184, C:D.184 PGE.5: 6 residues within 4Å: Chain C: H.17, E.108, H.111, P.112, H.150, E.154 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.111, C:H.150, C:E.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volkov, O.A. et al., Species-Selective Pyrimidineamine Inhibitors of Trypanosoma brucei S-Adenosylmethionine Decarboxylase. J. Med. Chem. (2018)

Release Date

2018-01-03

Peptides

S-adenosylmethionine decarboxylase beta chain: A
S-adenosylmethionine decarboxylase alpha chain: B
Inactive S-adenosylmethionine decarboxylase prozyme: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

S-adenosylmethionine decarboxylase beta chain

S-adenosylmethionine decarboxylase alpha chain

Inactive S-adenosylmethionine decarboxylase prozyme

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