Protein profile

KP13_00150

Glycerol kinase

Genome: KpKP13

Gene: glpK AHE42070.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GUW1
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Amino acids 503
Annotations 10
Features 24
PDB binders 14
Druggability 0.891

Overview

Basic information about this protein and its source genome.

Accession
KP13_00150
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
glpK AHE42070.1
Status
annotated
Amino acids
503
Structure source
AlphaFold + ColabFold
EC
2.7.1.30
GO
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. GO:0004370 Catalysis of the reaction: ATP + glycerol = sn-glycerol 3-phosphate + ADP + 2 H+. GO:0006072 The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
48.98
Human E-value
2.45e-07
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
63.232
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.51

Selected Druggability evidence

AlphaFold / UniProt model

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 0.891
Structure A0A0H3GUW1
Pocket Pocket 2
P2Rank 0.943
Structure A0A0H3GUW1
Pocket Pocket 1
ColabFold model
FPocket 0.827 · Pocket 7
P2Rank 0.94 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 2643 / 4744 genomes with a hit
Normalized 0.557

Sequence

Primary amino-acid sequence viewer.

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: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.
  • GO:0004370 Catalysis of the reaction: ATP + glycerol = sn-glycerol 3-phosphate + ADP + 2 H+.
  • GO:0006072 The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol.
  • 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:0046872 Binding to a metal ion.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
255 497 FunFam G3DSA:3.30.420.40:FF:000007 Glycerol kinase
6 253 Pfam PF00370 FGGY family of carbohydrate kinases, N-terminal domain
6 253 InterPro IPR018484 Carbohydrate kinase, FGGY, N-terminal
136 148 ProSitePatterns PS00933 FGGY family of carbohydrate kinases signature 1.
136 148 InterPro IPR018483 Carbohydrate kinase, FGGY, conserved site
5 497 NCBIfam TIGR01311 glycerol kinase GlpK
5 497 InterPro IPR005999 Glycerol kinase
5 256 SUPERFAMILY SSF53067 Actin-like ATPase domain
5 256 InterPro IPR043129 ATPase, nucleotide binding domain
363 383 ProSitePatterns PS00445 FGGY family of carbohydrate kinases signature 2.
363 383 InterPro IPR018483 Carbohydrate kinase, FGGY, conserved site
1 254 Gene3D G3DSA:3.30.420.40 -
4 498 Hamap MF_00186 Glycerol kinase [glpK].
4 498 InterPro IPR005999 Glycerol kinase
2 254 FunFam G3DSA:3.30.420.40:FF:000008 Glycerol kinase
6 492 CDD cd07786 FGGY_EcGK_like
256 498 SUPERFAMILY SSF53067 Actin-like ATPase domain
256 498 InterPro IPR043129 ATPase, nucleotide binding domain
7 497 PANTHER PTHR10196 SUGAR KINASE
4 503 PIRSF PIRSF000538 GlpK
4 503 InterPro IPR000577 Carbohydrate kinase, FGGY
255 501 Gene3D G3DSA:3.30.420.40 -
262 451 Pfam PF02782 FGGY family of carbohydrate kinases, C-terminal domain
262 451 InterPro IPR018485 Carbohydrate kinase, FGGY, C-terminal

3D Structure

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

3D visualization script Full viewer

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Structural evidence

0 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GUW1
AlphaFold — — full sequence — Viewing
ColabFold KP13_00150
ColabFold — — full sequence — Loaded
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
2 0.891

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 19.01 0.833
2 4.38 0.183
3 3.81 0.147
4 2.81 0.087
5 1.73 0.031

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.

64 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
6K76
O93623 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)…
BTB
3GG4
Q665C6 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
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
3LL3
Q5FM28 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.