SMTL ID : 4hkp.1

Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with CMP-N3-oxide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: K.74, I.131, A.134, K.135, F.139, L.140, D.170 Ligands: GOL.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.74, A:F.139, A:D.170 GOL.2: 6 residues within 4Å: Chain A: I.131, S.167, W.168, D.170, R.195 Ligands: GOL.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.168, A:R.195, A:R.195 GOL.3: 5 residues within 4Å: Chain A: K.82, P.107, S.108, E.296, R.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.82, A:P.107 GOL.6: 6 residues within 4Å: Chain B: K.74, A.134, K.135, F.139, L.140, D.170 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.74, B:A.134, B:K.135, B:K.135, B:F.139, B:D.170 GOL.7: 3 residues within 4Å: Chain B: L.253, E.254, A.255 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.253, B:A.255 Water bridges: B:S.266 GOL.8: 6 residues within 4Å: Chain B: S.58, Q.80, W.303, Y.306, L.307, L.310 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.80, B:Y.306 Water bridges: B:E.83, B:W.303

2 x TKW: 5-hydroxycytidine 5'-(dihydrogen phosphate)(Non-covalent)

TKW.4: 18 residues within 4Å: Chain A: S.89, D.91, K.113, H.115, D.144, K.146, M.203, S.204, I.233, P.249, Q.262, Y.264, G.282, R.283 Chain B: D.149, I.150, T.153 Ligands: 16B.5 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.89, A:K.113, A:K.146, A:S.204, A:S.204, A:Q.262, A:Y.264, A:G.282, A:R.283, B:T.153 Water bridges: A:G.250, A:G.250 Salt bridges: A:R.283 TKW.9: 19 residues within 4Å: Chain A: D.149, I.150, T.153 Chain B: S.89, D.91, K.113, H.115, D.144, K.146, M.203, S.204, I.233, P.249, G.250, Q.252, Q.262, Y.264, G.282, R.283 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.89, B:D.91, B:K.113, B:K.146, B:E.202, B:S.204, B:S.204, B:G.250, B:Q.262, B:Y.264, B:G.282, B:R.283, A:T.153 Water bridges: B:V.251 Salt bridges: B:R.283

1 x 16B: N-hydroxycytidine 5'-(dihydrogen phosphate)(Non-covalent)

16B.5: 19 residues within 4Å: Chain A: S.89, D.91, K.113, H.115, D.144, K.146, E.202, M.203, S.204, P.249, G.250, Q.262, Y.264, G.282, R.283 Chain B: D.149, I.150, T.153 Ligands: TKW.4 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.249 Hydrogen bonds: A:S.89, A:K.113, A:S.204, A:S.204, A:S.204, A:G.250, A:Q.262, A:Y.264, A:G.282, A:R.283, B:T.153 Water bridges: A:K.146, A:G.284 Salt bridges: A:R.283

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Purohit, M.K. et al., Novel cytidine-based orotidine-5'-monophosphate decarboxylase inhibitors with an unusual twist. J.Med.Chem. (2012)

Release Date

2012-11-14

Peptides

Uridine 5'-monophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uridine 5'-monophosphate synthase

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