Protein target profile

VK055_2800

ornithine carbamoyltransferase

Genome: KpATCC43816 Gene: AIK81389.1 argF 3D evidence: Experimental + ColabFold model Metabolism 1 reaction UniProt A0A0H3GHJ1
Length 334
Pocket druggability 0.453
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 65 total records
Functional annotation 1 EC 8 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
Hit
Human identity (%)
36.89 Lower values reduce human off-target concern.
Human E-value
2.9500000000000004e-56
Gut microbiome similarity
42.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.21 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.453
Structure 7TMD
Pocket Pocket 1
P2Rank 0.436
Structure 7TMD
Pocket Pocket 1
ColabFold model
FPocket 0.922 · Pocket 1
P2Rank 0.699 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 1998 / 4744 genomes with a hit
Prevalence 42.1%

Cross-references

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

Structure

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Metabolic context: more central than 94.2% of genes in this genome.

Relative network centrality 94.2% more central than 94.2% of genes in this genome
Chokepoint Not a chokepoint
Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSAFYQKHFLKLLDFTPAEITALLELAAKLKADKKNGIEVQKLAGKNIALIFEKDSTRTRCSFEVAAYDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLAQYAGVPVWNGLTNEFHPTQLLADLLTMKEHLPGKAFNQMTLVYAGDARNNMGNSMLEAAALTGLDLRLVAPSACWPEAALVETCTALAKQQGGNITLTEDIAAGVKGADFIYTDVWVSMGEAKEKWAERIALLRDYQVNSAMLALTGNPQVKFLHCLPAFHDDQTTLGKQMAADYGLHGGMEVTDEVFESAASVVFDQAENRMHTIKAVMVATLSR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0016743 Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor).
  • GO:0006591 The chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis.
  • GO:0016597 Binding to an amino acid, organic acids containing one or more amino substituents.
  • GO:0004585 Catalysis of the reaction: carbamoyl phosphate + L-ornithine = phosphate + L-citrulline.
  • GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0019240 The chemical reactions and pathways resulting in the formation of citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins.
  • 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.

36 records
Show feature table
Start End DB Term Name
6 332 Gene3D G3DSA:3.40.50.1370 Aspartate/ornithine carbamoyltransferase
6 332 InterPro IPR036901 Aspartate/ornithine carbamoyltransferase superfamily
229 239 PRINTS PR00102 Ornithine carbamoyltransferase signature
229 239 InterPro IPR002292 Ornithine/putrescine carbamoyltransferase
83 96 PRINTS PR00102 Ornithine carbamoyltransferase signature
83 96 InterPro IPR002292 Ornithine/putrescine carbamoyltransferase
123 137 PRINTS PR00102 Ornithine carbamoyltransferase signature
123 137 InterPro IPR002292 Ornithine/putrescine carbamoyltransferase
50 64 PRINTS PR00102 Ornithine carbamoyltransferase signature
50 64 InterPro IPR002292 Ornithine/putrescine carbamoyltransferase
311 322 PRINTS PR00102 Ornithine carbamoyltransferase signature
311 322 InterPro IPR002292 Ornithine/putrescine carbamoyltransferase
152 319 FunFam G3DSA:3.40.50.1370:FF:000004 Ornithine carbamoyltransferase
52 71 PRINTS PR00100 Aspartate/ornithine carbamoyltransferase superfamily signature
52 71 InterPro IPR006130 Aspartate/ornithine carbamoyltransferase
134 145 PRINTS PR00100 Aspartate/ornithine carbamoyltransferase superfamily signature
134 145 InterPro IPR006130 Aspartate/ornithine carbamoyltransferase
297 320 PRINTS PR00100 Aspartate/ornithine carbamoyltransferase superfamily signature
297 320 InterPro IPR006130 Aspartate/ornithine carbamoyltransferase
267 276 PRINTS PR00100 Aspartate/ornithine carbamoyltransferase superfamily signature
267 276 InterPro IPR006130 Aspartate/ornithine carbamoyltransferase
7 147 Pfam PF02729 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
7 147 InterPro IPR006132 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding
156 330 Pfam PF00185 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
156 330 InterPro IPR006131 Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain
152 319 Gene3D G3DSA:3.40.50.1370 Aspartate/ornithine carbamoyltransferase
152 319 InterPro IPR036901 Aspartate/ornithine carbamoyltransferase superfamily
7 332 NCBIfam TIGR00658 ornithine carbamoyltransferase
7 332 InterPro IPR002292 Ornithine/putrescine carbamoyltransferase
2 333 SUPERFAMILY SSF53671 Aspartate/ornithine carbamoyltransferase
2 333 InterPro IPR036901 Aspartate/ornithine carbamoyltransferase superfamily
6 333 Hamap MF_01109 Ornithine carbamoyltransferase, catabolic [argI].
6 333 InterPro IPR024904 Ornithine carbamoyltransferase
52 59 ProSitePatterns PS00097 Aspartate and ornithine carbamoyltransferases signature.
52 59 InterPro IPR006130 Aspartate/ornithine carbamoyltransferase
3 333 PANTHER PTHR45753 ORNITHINE CARBAMOYLTRANSFERASE, MITOCHONDRIAL

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.

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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 · FPocket

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

Site 1 FPocket #1
0.453
Show in viewer
Surrounding area
Site 2 FPocket #2
0.45
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.436
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.005
Show in viewer
Surrounding area
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 7TMD
X-ray 2.35 Å A,B,C,D,E,F
100.0% 1-334
Viewing
ColabFold VK055_2800
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.

65 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 15 records from similar proteins
Structural ligands 15 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
1NP PDB via homolog 144.2 Da · LogP 2.55 · TPSA 20.2 Open detail RCSB PDB
8H8 PDB via homolog Detail RCSB PDB
98T PDB via homolog Detail RCSB PDB
CIR PDB via homolog Detail RCSB PDB
CP 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
1NP RCSB PDB P9WIT9 144.2 Da LogP 2.55 TPSA 20.2 ✓ Ro5 ✓ Clean c1ccc2c(c1)cccc2O
8H8 RCSB PDB P9WIT9 137.1 Da LogP 1.40 TPSA 44.0 ✓ Ro5 ✓ Clean c1cc(c(cc1O)F)C#N
98T RCSB PDB P9WIT9 278.0 Da LogP 1.78 TPSA 46.5 ✓ Ro5 ✓ Clean COC(=O)c1ccc(c(c1)I)O
CIR RCSB PDB Q8DCF5 175.2 Da LogP -1.15 TPSA 118.4 ✓ Ro5 ✓ Clean C(C[C@@H](C(=O)O)N)CNC(=O)N
CP RCSB PDB Q8DCF5 141.0 Da LogP -0.83 TPSA 109.9 ✓ Ro5 ✓ Clean C(=O)(N)OP(=O)(O)O
NMR RCSB PDB P9WIT9 B(=O)(c1cc(cc(c1)Cl)Cl)O
NVA RCSB PDB Q81M99 117.1 Da LogP 0.20 TPSA 63.3 ✓ Ro5 ✓ Clean CCC[C@@H](C(=O)O)N
PAO RCSB PDB P04391 254.2 Da LogP -1.53 TPSA 149.9 ✓ Ro5 ✓ Clean C(C[C@@H](C(=O)O)N)CNC(=O)CP(=O)(O)O
PE5 RCSB PDB Q8DCF5 398.5 Da LogP 0.13 TPSA 94.1 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCOCCO
PSQ RCSB PDB P04391 290.2 Da LogP -1.77 TPSA 184.8 1 viol. ✓ Clean C(C[C@@H](C(=O)O)N)CN[P@](=O)(N)NS(=O)(=O)O
PTZ RCSB PDB P9WIT9 190.3 Da LogP 2.70 TPSA 38.9 ✓ Ro5 ✓ Clean Cc1c(nc(s1)N)c2ccccc2
PUW RCSB PDB Q837U7 210.2 Da LogP -0.98 TPSA 112.7 ✓ Ro5 ✓ Clean C(CCNC(=O)CP(=O)(O)O)CN
UJZ RCSB PDB P9WIT9 265.0 Da LogP 3.34 TPSA 28.7 ✓ Ro5 ✓ Clean c1c(cc(c2c1[nH]cn2)Br)C(F)(F)F
UK2 RCSB PDB P9WIT9 181.0 Da LogP -0.42 TPSA 83.6 ✓ Ro5 ✓ Clean B(c1ccc(c(c1)[N+](=O)[O-])C)(O)O
UKH RCSB PDB P9WIT9 166.9 Da LogP -0.73 TPSA 83.6 ✓ Ro5 ✓ Clean B(c1ccc(cc1)[N+](=O)[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.