SMTL ID : 3mo7.1

Crystal structure of human orotidine 5'-monophosphate decarboxylase covalently modified by 2'-fluoro-6-iodo-UMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

2 x UFT: 2'-deoxy-2'-fluorouridine 5'-(dihydrogen phosphate)(Covalent)

UFT.1: 17 residues within 4Å: Chain A: S.56, D.58, K.80, H.82, D.111, K.113, M.170, S.171, P.216, Q.229, Y.231, V.248, G.249, R.250 Chain B: D.116, I.117, T.120 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.56, A:K.80, A:S.171, A:S.171, A:S.171, A:Q.229, A:Y.231, A:Y.231, A:G.249, A:R.250, B:T.120 Water bridges: A:G.217, A:G.217 Salt bridges: A:R.250 UFT.3: 17 residues within 4Å: Chain A: D.116, I.117, T.120 Chain B: S.56, D.58, K.80, H.82, D.111, K.113, M.170, S.171, P.216, Q.229, Y.231, V.248, G.249, R.250 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.56, B:D.58, B:K.80, B:D.111, B:S.171, B:S.171, B:S.171, B:Q.229, B:Y.231, B:Y.231, B:Y.231, B:G.249, B:R.250, A:T.120, A:T.120 Water bridges: B:G.217, B:G.217 Salt bridges: B:R.250

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: K.41, I.98, A.101, F.106, L.107, D.137 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.41, A:K.41, A:A.101, A:F.106 Water bridges: A:D.137, A:D.137, A:D.137 GOL.4: 6 residues within 4Å: Chain B: K.41, I.98, A.101, F.106, L.107, D.137 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.41, B:K.41, B:A.101, B:F.106 Water bridges: B:D.137, B:D.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lewis, M. et al., Novel interactions of fluorinated nucleotide derivatives targeting orotidine 5'-monophosphate decarboxylase. J.Med.Chem. (2011)

Release Date

2011-04-06

Peptides

Uridine 5'-monophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Uridine 5'-monophosphate synthase

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