KpKP13 Protein target profile

Acetylglutamate kinase

Accession: KP13_00555

Gene: argB AHE47031.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GPQ8
Length 259
Pocket druggability (P2Rank · AlphaFold DB model) 0.888
Direct ligand evidence 0 70 total records
Functional annotation 1 EC 5 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
2.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
94.76 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.888
Structure A0A0H3GPQ8
Pocket Pocket 1
Druggability (FPocket) 0.386
Structure A0A0H3GPQ8
Pocket Pocket 2
ColabFold model
P2Rank 0.915 · Pocket 1
FPocket 0.308 · Pocket 13
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 129 / 4744 genomes with a hit
Prevalence 2.7%

Sequence

Primary amino-acid sequence viewer.

MMMNPLIIKLGGVLLDSEEALERLFTALVNYREAHQRPLIIVHGGGCVVDELMKQLNLPVQKKNGLRVTPAEQIDIITGALAGTANKTLLAWAKKHGISSVGLFLGDGDSVKVTQLDAELGHVGLAQPGSPALINTLLAGGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLSDVSGILDGKGQRIAEMTAEKAEQLIEQGIITDGMIVKVNAALDAARALGRPVDIASWRHAEQLPALFNGTPIGTRILA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0006526 The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
  • GO:0003991 Catalysis of the reaction: ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamate-5-phosphate.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0042450 OBSOLETE. The chemical reactions and pathways resulting in the formation of arginine (2-amino-5-guanidinopentanoic acid) via the intermediate compound ornithine.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
6 257 CDD cd04249 AAK_NAGK-NC
6 257 InterPro IPR041731 N-Acetyl-L-glutamate kinase, noncyclic
16 20 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
6 15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 20 Phobius SIGNAL_PEPTIDE Signal peptide region
1 5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 259 PIRSF PIRSF000728 NAGK
1 259 InterPro IPR004662 Acetylglutamate kinase family
6 236 Pfam PF00696 Amino acid kinase family
6 236 InterPro IPR001048 Aspartate/glutamate/uridylate kinase
2 259 Gene3D G3DSA:3.40.1160.10 -
2 259 InterPro IPR036393 Acetylglutamate kinase-like superfamily
6 235 NCBIfam TIGR00761 acetylglutamate kinase
6 235 InterPro IPR004662 Acetylglutamate kinase family
21 259 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
6 257 PANTHER PTHR23342 N-ACETYLGLUTAMATE SYNTHASE
2 259 FunFam G3DSA:3.40.1160.10:FF:000008 Acetylglutamate kinase
3 252 Hamap MF_00082 Acetylglutamate kinase [argB].
3 252 InterPro IPR037528 Acetylglutamate kinase ArgB
2 257 SUPERFAMILY SSF53633 Carbamate kinase-like
2 257 InterPro IPR036393 Acetylglutamate kinase-like superfamily

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.888
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.033
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #2
0.386 Unusual size
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:157-157
UniProt: Binding site:180-185
UniProt: Binding site:208-210
UniProt: Binding site:43-44
UniProt: Binding site:65-65
UniProt: Site:216-216 Transition state stabilizer
UniProt: Site:7-7 Transition state stabilizer
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GPQ8
AlphaFold DB full sequence Viewing
ColabFold KP13_00555
ColabFold full sequence Loaded

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.

70 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 20 records from similar proteins
Structural ligands 20 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
14N PDB via homolog 220.3 Da · LogP 1.14 · TPSA 43.8 Open detail RCSB PDB
5RN PDB via homolog Detail RCSB PDB
97Q PDB via homolog Detail RCSB PDB
97T PDB via homolog Detail RCSB PDB
97W PDB via homolog Detail RCSB PDB

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
14N RCSB PDB P9WQ01 220.3 Da LogP 1.14 TPSA 43.8 ✓ Ro5 ✓ Clean CN1CCN(CC1)c2ccc(cc2)C(=O)O
5RN RCSB PDB P9WQ01 159.2 Da LogP 2.37 TPSA 32.9 ✓ Ro5 ✓ Clean CC(=O)c1c[nH]c2c1cccc2
97Q RCSB PDB P9WQ01 281.2 Da LogP 3.98 TPSA 33.1 ✓ Ro5 ✓ Clean c1cc2c(cc(nc2c(c1)C(F)(F)F)C(F)(F)F)O
97T RCSB PDB P9WQ01 161.2 Da LogP 2.05 TPSA 46.3 ✓ Ro5 ✓ Clean c1ccc(c(c1)c2ccno2)O
97W RCSB PDB P9WQ01 213.2 Da LogP 2.96 TPSA 33.1 ✓ Ro5 ✓ Clean c1cc2c(ccnc2cc1C(F)(F)F)O
98K RCSB PDB P9WQ01 152.6 Da LogP 2.22 TPSA 28.7 ✓ Ro5 ✓ Clean c1ccc2c(c1)[nH]c(n2)Cl
98Q RCSB PDB P9WQ01 215.2 Da LogP 3.20 TPSA 25.0 ✓ Ro5 ✓ Clean COc1cc2cc[nH]c2cc1C(F)(F)F
98T RCSB PDB P9WQ01 278.0 Da LogP 1.78 TPSA 46.5 ✓ Ro5 ✓ Clean COC(=O)c1ccc(c(c1)I)O
98W RCSB PDB P9WQ01 210.2 Da LogP 0.97 TPSA 72.8 ✓ Ro5 ✓ Clean COC(=O)c1cc(cc(c1)O)C(=O)OC
98Z RCSB PDB P9WQ01 142.2 Da LogP 2.04 TPSA 39.6 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)C#N
9EQ RCSB PDB P9WQ01 152.1 Da LogP 1.30 TPSA 57.5 ✓ Ro5 ✓ Clean CC(=O)c1c(cccc1O)O
ANP RCSB PDB P0A6C8 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)…
DTU RCSB PDB P0A6C8 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@H]([C@H](CS)O)O)S
GGB RCSB PDB P9WQ01 176.2 Da LogP -1.80 TPSA 134.5 ✓ Ro5 ✓ Clean [H]/N=C(\N)/NOCC[C@@H](C(=O)O)N
NHE RCSB PDB P9WQ01 207.3 Da LogP 0.80 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCS(=O)(=O)O
NLG RCSB PDB P0A6C8 189.2 Da LogP -0.56 TPSA 103.7 ✓ Ro5 ✓ Clean CC(=O)N[C@@H](CCC(=O)O)C(=O)O
PIY RCSB PDB P9WQ01 144.2 Da LogP 2.08 TPSA 28.7 ✓ Ro5 ✓ Clean c1ccc(cc1)c2[nH]ccn2
SRT RCSB PDB Q8ZA87 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@H]([C@H](C(=O)O)O)(C(=O)O)O
UOK RCSB PDB P9WQ01 186.2 Da LogP 2.24 TPSA 48.8 ✓ Ro5 ✓ Clean COc1ccc2c(c1)c(c[nH]2)CC#N
X2W RCSB PDB P0A6C8 269.1 Da LogP -1.01 TPSA 150.2 ✓ Ro5 ✓ Clean CC(=O)N[C@@H](CCC(=O)OP(=O)(O)O)C(=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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.