Protein profile

PA3579

glycerol kinase

Genome: NC_002516.2

Gene: glpK2 glpK1 PA3579 Structure source: AlphaFold UniProt Q9HY41
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Amino acids 494
Annotations 10
Features 22
PDB binders 13
Druggability 0.732

Overview

Basic information about this protein and its source genome.

Accession
PA3579
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
glpK2 glpK1 PA3579
Status
annotated
Amino acids
494
Structure source
AlphaFold
EC
2.7.1.30
GO
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0004370 Catalysis of the reaction: ATP + glycerol = sn-glycerol 3-phosphate + ADP + 2 H+. GO:0019563 The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids. GO:0006071 The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids. GO:0006072 The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
48.98
Human E-value
1.3e-06
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.732
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MSHYLLAIDQGTTSSRAIVFSAQGLPVASCQQEFKQYFPKDGWVEHDGEEIWLTTLQVCRDALARKGLRAADIAAIGITNQRETTLVWDAASGDLIHPAIVWQDRRTADYCAELKAAGHEANVSARTGLLIDPYFSATKLRWILDNVPGARQRAERGELRFGTVDCFLLWRLTGGRSHRTDATNASRTLLFNIHSQDWDEELLALFEIPRSLLPEVLDCAAEFGVSEPSLLGAAIPVLGMAGDQQAALIGQACFQPGMVKSTYGTGCFMIQNTGEQPVTSKNRLLTTVGYRLDGKVSYAVEGSIFVAGAAVQWLRDGIKLIDHAHESEALAIQAGDSNGVYLVPAFTGLGAPYWDPKARGAIFGLTRDTGIKEIVTAGLQSVCYQTRDLLEAMRQDGTPPSALRVDGGMVVNNWMMQFLTDILGVTVERPEVTETTALGVAYMAGLKAGFYRDLDDIASHWHLQRRFAAHMAEERRGELYAGWQNAVRRVRSEA

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0004370 Catalysis of the reaction: ATP + glycerol = sn-glycerol 3-phosphate + ADP + 2 H+.
  • GO:0019563 The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
  • GO:0006071 The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
  • GO:0006072 The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol.
  • GO:0016773 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
  • GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
4 250 Pfam PF00370 FGGY family of carbohydrate kinases, N-terminal domain
4 250 InterPro IPR018484 Carbohydrate kinase, FGGY, N-terminal
2 494 PIRSF PIRSF000538 GlpK
2 494 InterPro IPR000577 Carbohydrate kinase, FGGY
260 446 Pfam PF02782 FGGY family of carbohydrate kinases, C-terminal domain
260 446 InterPro IPR018485 Carbohydrate kinase, FGGY, C-terminal
4 488 CDD cd07786 FGGY_EcGK_like
5 489 PANTHER PTHR10196 SUGAR KINASE
4 491 NCBIfam TIGR01311 glycerol kinase GlpK
4 491 InterPro IPR005999 Glycerol kinase
2 494 Hamap MF_00186 Glycerol kinase [glpK].
2 494 InterPro IPR005999 Glycerol kinase
4 253 SUPERFAMILY SSF53067 Actin-like ATPase domain
4 253 InterPro IPR043129 ATPase, nucleotide binding domain
252 493 FunFam G3DSA:3.30.420.40:FF:000007 Glycerol kinase
134 146 ProSitePatterns PS00933 FGGY family of carbohydrate kinases signature 1.
134 146 InterPro IPR018483 Carbohydrate kinase, FGGY, conserved site
2 251 Gene3D G3DSA:3.30.420.40 -
252 491 Gene3D G3DSA:3.30.420.40 -
253 492 SUPERFAMILY SSF53067 Actin-like ATPase domain
253 492 InterPro IPR043129 ATPase, nucleotide binding domain
1 251 FunFam G3DSA:3.30.420.40:FF:000008 Glycerol kinase

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA3579
AlphaFold — — full sequence — Viewing
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
1 0.732
2 0.362

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

63 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
4NP
5AZI
D3KVM3 219.1 Da LogP 1.07 TPSA 109.9 ✓ Ro5 ✓ Clean c1cc(ccc1[N+](=O)[O-])OP(=O)(O)O
6XZ
5GN5
D3KVM3 382.4 Da LogP 2.54 TPSA 86.4 ✓ Ro5 Alert COc1ccc(cc1)N2CCN(CC2)CC3=CC(=O)Oc4c3ccc(c4O)O
6Y0
5GN6
D3KVM3 234.3 Da LogP 2.55 TPSA 70.7 ✓ Ro5 Alert CCCCC1=CC(=O)Oc2c1ccc(c2O)O
ACP
1GLL
P0A6F3 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP
6J9Q
D3KVM3 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ATF
1BWF
P0A6F3 541.2 Da LogP -0.93 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ATS
1GLJ
P0A6F3 549.2 Da LogP -2.76 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
DXP
3LL3
Q5FM28 214.1 Da LogP -1.59 TPSA 124.3 ✓ Ro5 ✓ Clean CC(=O)[C@H]([C@@H](COP(=O)(O)O)O)O
G3H
1GLC
P0A6F3 170.1 Da LogP -1.34 TPSA 104.1 ✓ Ro5 ✓ Clean C([C@H](C=O)O)OP(=O)(O)O
G3P
3WXJ
D3KVM3 172.1 Da LogP -1.55 TPSA 107.2 ✓ Ro5 ✓ Clean C([C@H](COP(=O)(O)O)O)O
NH4
2ITM
P09099 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
POP
6JAF
D3KVM3 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
XUL
2ITM
P09099 150.1 Da LogP -2.74 TPSA 98.0 ✓ Ro5 ✓ Clean C([C@H]([C@@H](C(=O)CO)O)O)O

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.