SMTL ID : 5ajv.1

Human PFKFB3 in complex with an indole inhibitor 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 10 residues within 4Å: Chain A: L.43, P.44, A.45, R.46, G.47, K.48, T.49, N.164, K.169 Ligands: PO4.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:A.45, A:R.46, A:G.47, A:K.48, A:T.49, A:N.164 Water bridges: A:K.48, A:K.48 Salt bridges: A:K.48, A:K.169 PO4.2: 4 residues within 4Å: Chain A: V.71, R.99, T.127, Y.194 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.127, A:T.127, A:Y.194 Salt bridges: A:R.99 PO4.3: 6 residues within 4Å: Chain A: T.49, N.70, D.125, K.169, Y.425 Ligands: PO4.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.49, A:N.70, A:Y.425 Salt bridges: A:K.169 PO4.6: 10 residues within 4Å: Chain B: L.43, P.44, A.45, R.46, G.47, K.48, T.49, N.164, K.169 Ligands: PO4.8 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:A.45, B:R.46, B:G.47, B:K.48, B:T.49, B:T.49, B:N.164 Water bridges: B:K.48, B:K.48 Salt bridges: B:K.48, B:K.169 PO4.7: 4 residues within 4Å: Chain B: V.71, R.99, T.127, Y.194 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.127, B:T.127 Water bridges: B:Y.194 Salt bridges: B:R.99 PO4.8: 6 residues within 4Å: Chain B: T.49, N.70, D.125, K.169, Y.425 Ligands: PO4.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.49, B:N.70 Salt bridges: B:K.169

2 x 8R2: (2S)-2-amino-N-[4-[(2-amino-3-cyano-1H-indol-5-yl)oxy]phenyl]-3-hydroxy-propanamide(Non-covalent)

8R2.4: 18 residues within 4Å: Chain A: A.45, R.46, G.47, Y.50, I.51, S.153, C.155, V.160, N.164, V.215, V.218, G.219, F.222, L.239, M.240, I.242, V.244 Chain B: V.227 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.50, A:I.51, A:V.215, A:V.218, A:I.242, A:V.244 Hydrogen bonds: A:A.45, A:N.164, A:L.239, A:I.242 8R2.9: 18 residues within 4Å: Chain A: V.227 Chain B: A.45, R.46, G.47, Y.50, I.51, S.153, C.155, V.160, N.164, V.215, V.218, G.219, F.222, L.239, M.240, I.242, V.244 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.50, B:I.51, B:V.215, B:V.218, B:I.242, B:V.244 Hydrogen bonds: B:A.45, B:N.164, B:L.239, B:I.242

2 x FDP: 2,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FDP.5: 15 residues within 4Å: Chain A: R.253, H.254, N.257, N.260, I.265, G.266, E.323, Y.334, R.348, K.352, Y.363, H.388, Q.389, R.393, T.441 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.257, A:N.260, A:G.266, A:Y.334, A:Y.334, A:Y.363, A:Q.389, A:Q.389 Salt bridges: A:R.253, A:H.254, A:R.348, A:K.352, A:H.388, A:R.393 FDP.10: 15 residues within 4Å: Chain B: R.253, H.254, N.257, N.260, I.265, G.266, E.323, Y.334, R.348, K.352, Y.363, H.388, Q.389, R.393, T.441 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:N.257, B:N.260, B:G.266, B:E.323, B:Y.334, B:Y.334, B:Q.389, B:Q.389 Salt bridges: B:R.253, B:H.254, B:R.348, B:K.352, B:H.388, B:R.393

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boyd, S. et al., Structure-Based Design of Potent and Selective Inhibitors of the Metabolic Kinase Pfkfb3. J.Med.Chem. (2015)

Release Date

2015-04-22

Peptides

HUMAN PFKFB3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

HUMAN PFKFB3

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