SMTL ID : 5ak0.1

Human PFKFB3 in complex with an indole inhibitor 6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-dimer

Ligands

2 x PHS: PHOSPHONIC ACID(Non-covalent)

PHS.1: 6 residues within 4Å: Chain A: R.253, H.254, N.260, H.388, Q.389 Ligands: F6P.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.260, A:E.323, A:Q.389 Water bridges: A:H.388 Salt bridges: A:R.253, A:H.254, A:H.388 PHS.6: 6 residues within 4Å: Chain B: R.253, H.254, N.260, H.388, Q.389 Ligands: F6P.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.260, B:Q.389 Salt bridges: B:R.253, B:H.254, B:H.388

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

PO4.2: 8 residues within 4Å: Chain A: L.43, P.44, A.45, R.46, G.47, K.48, T.49, K.169 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:L.43, A:A.45, A:R.46, A:G.47, A:K.48, A:T.49, A:T.49 Water bridges: A:G.47, A:K.48, A:Y.50 Salt bridges: A:K.48, A:K.169 PO4.3: 4 residues within 4Å: Chain A: V.71, F.88, R.99, Y.194 8 PLIP interactions: 8 interactions with chain A Water bridges: A:T.127, A:T.127, A:T.127, A:T.127, A:R.133, A:R.190, A:Y.194 Salt bridges: A:R.99 PO4.7: 8 residues within 4Å: Chain B: L.43, P.44, A.45, R.46, G.47, K.48, T.49, K.169 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:L.43, B:A.45, B:R.46, B:G.47, B:K.48, B:T.49 Water bridges: B:G.47, B:K.48, B:Y.50 Salt bridges: B:K.48, B:K.169 PO4.8: 4 residues within 4Å: Chain B: V.71, F.88, R.99, Y.194 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.194 Water bridges: B:T.127, B:T.127, B:T.127, B:T.127, B:R.133, B:R.190 Salt bridges: B:R.99

2 x F6P: 6-O-phosphono-beta-D-fructofuranose(Non-covalent)

F6P.4: 11 residues within 4Å: Chain A: N.260, I.265, G.266, E.323, Y.334, R.348, K.352, Y.363, Q.389, R.393 Ligands: PHS.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.266, A:E.323, A:Y.334, A:Q.389, A:Q.389 Water bridges: A:N.260, A:N.260, A:G.266, A:Y.334, A:Y.334, A:R.348, A:Y.357, A:H.388, A:R.393 Salt bridges: A:R.348, A:K.352, A:R.393 F6P.9: 11 residues within 4Å: Chain B: N.260, I.265, G.266, E.323, Y.334, R.348, K.352, Y.363, Q.389, R.393 Ligands: PHS.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.266, B:Y.334, B:Y.334, B:Y.363, B:Q.389, B:Q.389 Water bridges: B:N.260, B:N.260, B:G.266, B:R.348, B:H.388, B:R.393 Salt bridges: B:R.348, B:K.352, B:R.393

2 x 8V1: (2S)-N-[4-[1-METHYL-3-(1-METHYLPYRAZOL-4-YL)INDOL-5-YL]OXYPHENYL]PYRROLIDINE-2-CARBOXAMIDE(Non-covalent)

8V1.5: 19 residues within 4Å: Chain A: A.45, R.46, G.47, Y.50, I.51, S.153, C.155, S.163, I.165, V.218, G.219, F.222, L.239, M.240, I.242, H.243, V.244, A.424 Chain B: V.227 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.50, A:I.165, A:V.218, A:V.218, A:F.222, A:I.242, A:I.242 Hydrogen bonds: A:L.239 pi-Stacking: A:Y.50 8V1.10: 19 residues within 4Å: Chain A: V.227 Chain B: A.45, R.46, G.47, Y.50, I.51, S.153, C.155, S.163, I.165, V.218, G.219, F.222, L.239, M.240, I.242, H.243, V.244, A.424 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.50, B:I.165, B:V.218, B:V.218, B:F.222, B:I.242, B:I.242 Hydrogen bonds: B:L.239 pi-Stacking: B:Y.50

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

6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE 3

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