Protein target profile

KP13_01965

Carbamoyl-phosphate synthase small chain

Genome: KpKP13 Gene: carA AHE46404.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GI28
Length 391
Pocket druggability 0.232
Direct ligand evidence 0 71 total records
Functional annotation 1 EC 7 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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 (%)
38.743 Lower values reduce human off-target concern.
Human E-value
1.3199999999999998e-68
Gut microbiome similarity
5.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
72.296 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.64 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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 0.232
Structure A0A0H3GI28
Pocket Pocket 5
P2Rank 0.601
Structure A0A0H3GI28
Pocket Pocket 1
ColabFold model
FPocket 0.381 · Pocket 5
P2Rank 0.684 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 248 / 4744 genomes with a hit
Prevalence 5.2%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MSGYSLEDVLIKSALLVLEDGTQFHGRAIGATGTAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVGTNAADEESSQVHAQGLVIRDLPLIASNFRSTEDLSSYLKRHNIVAIADIDTRKLTRLLREKGAQNGCIIAGDSPDAQLALEKAKAFPGLNGMDLAKEVTTAETYSWTQGSWTLAGDLPEAKAESELPFHVVAYDFGAKRNILRMLVDRGCRLTVVPAKTSAADVLALNPDGIFLSNGPGDPAPCDYAIEAIEKFLETDIPVFGICLGHQLLALASGAKTIKMKFGHHGGNHPVKDIDNNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHDAAPLFNHFIELIELYRQSAK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0004088 Catalysis of the reaction: hydrogencarbonate + L-glutamine + 2 ATP + H2O = carbamoyl phosphate + L-glutamate + 2 ADP + phosphate + 2 H+.
  • GO:0006207 The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
  • GO:0006541 The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0004359 Catalysis of the reaction: L-glutamine + H2O = L-glutamate + NH4+.
  • GO:0044205 The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD+ or oxygen.
  • GO:0006526 The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

35 records
Show feature table
Start End DB Term Name
245 254 PRINTS PR00096 Glutamine amidotransferase superfamily signature
358 371 PRINTS PR00096 Glutamine amidotransferase superfamily signature
273 284 PRINTS PR00096 Glutamine amidotransferase superfamily signature
203 380 CDD cd01744 GATase1_CPSase
203 380 InterPro IPR035686 Carbamoyl-phosphate synthase small subunit, GATase1 domain
12 153 SUPERFAMILY SSF52021 Carbamoyl phosphate synthetase, small subunit N-terminal domain
12 153 InterPro IPR036480 Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily
12 142 SMART SM01097 CPSase_sm_chain_2
12 142 InterPro IPR002474 Carbamoyl-phosphate synthase small subunit, N-terminal domain
242 256 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature
203 217 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature
273 289 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature
315 326 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature
290 307 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature
206 381 Pfam PF00117 Glutamine amidotransferase class-I
206 381 InterPro IPR017926 Glutamine amidotransferase
161 387 Gene3D G3DSA:3.40.50.880 -
161 387 InterPro IPR029062 Class I glutamine amidotransferase-like
12 368 PANTHER PTHR11405 CARBAMOYLTRANSFERASE FAMILY MEMBER
14 384 NCBIfam TIGR01368 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit
14 384 InterPro IPR006274 Carbamoyl-phosphate synthase, small subunit
11 160 FunFam G3DSA:3.50.30.20:FF:000001 Carbamoyl-phosphate synthase small chain
162 383 SUPERFAMILY SSF52317 Class I glutamine amidotransferase-like
162 383 InterPro IPR029062 Class I glutamine amidotransferase-like
161 388 FunFam G3DSA:3.40.50.880:FF:000011 Carbamoyl-phosphate synthase small chain
12 387 Hamap MF_01209 Carbamoyl-phosphate synthase small chain [carA].
12 387 InterPro IPR006274 Carbamoyl-phosphate synthase, small subunit
11 160 Gene3D G3DSA:3.50.30.20 -
11 160 InterPro IPR036480 Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily
202 389 ProSiteProfiles PS51273 Glutamine amidotransferase type 1 domain profile.
16 141 Pfam PF00988 Carbamoyl-phosphate synthase small chain, CPSase domain
16 141 InterPro IPR002474 Carbamoyl-phosphate synthase small subunit, N-terminal domain
245 254 PRINTS PR00097 Anthranilate synthase component II signature
358 371 PRINTS PR00097 Anthranilate synthase component II signature
273 284 PRINTS PR00097 Anthranilate synthase component II signature

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 #5
0.232
Likely same site as P2Rank 2 0.7 Å 12 shared residues 92% of smaller site
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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.601
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Surrounding area
Site 2 P2Rank #2
0.563
Likely same site as FPocket 5 0.7 Å 12 shared residues 92% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.298
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Surrounding area
Site 4 P2Rank #4
0.256
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Surrounding area
Site 5 P2Rank #5
0.071
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Surrounding area
Residue sets
UniProt: Active site:269-269 Nucleophile
UniProt: Active site:353-353
UniProt: Active site:355-355
UniProt: Binding site:241-241
UniProt: Binding site:243-243
UniProt: Binding site:270-270
UniProt: Binding site:273-273
UniProt: Binding site:311-311
UniProt: Binding site:313-313
UniProt: Binding site:314-314
UniProt: Binding site:47-47
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_A0A0H3GI28
AlphaFold DB full sequence Viewing
ColabFold KP13_01965
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.

71 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 21 records from similar proteins
Structural ligands 14 0 loaded crystals
Measured bioactivity 7 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
0L1 PDB via homolog 146.1 Da · LogP 0.72 · TPSA 74.6 Open detail RCSB PDB
374 PDB via homolog Detail RCSB PDB
3NP PDB via homolog Detail RCSB PDB
F9V PDB via homolog Detail RCSB PDB
GUA 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
0L1 RCSB PDB P31327 146.1 Da LogP 0.72 TPSA 74.6 ✓ Ro5 ✓ Clean C(CCC(=O)O)CC(=O)O
374 RCSB PDB P31327 418.4 Da LogP 3.36 TPSA 59.1 ✓ Ro5 ✓ Clean C[C@@H]1CN(C[C@H](N1C(=O)c2ccc(cc2F)OC)C)C(=O)c…
3NP RCSB PDB P31327 119.1 Da LogP -0.26 TPSA 80.4 ✓ Ro5 ✓ Clean C(C[N+](=O)[O-])C(=O)O
F9V RCSB PDB P31327 194.2 Da LogP 1.33 TPSA 74.6 ✓ Ro5 ✓ Clean c1ccc(cc1)C(CC(=O)O)C(=O)O
GUA RCSB PDB P31327 132.1 Da LogP 0.33 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)CC(=O)O
IMP RCSB PDB P0A6F1 348.2 Da LogP -2.15 TPSA 180.0 ✓ Ro5 ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…
JO3 RCSB PDB P31327 132.1 Da LogP 0.18 TPSA 74.6 ✓ Ro5 ✓ Clean CC(CC(=O)O)C(=O)O
NLG RCSB PDB P31327 189.2 Da LogP -0.56 TPSA 103.7 ✓ Ro5 ✓ Clean CC(=O)N[C@@H](CCC(=O)O)C(=O)O
NX6 RCSB PDB P31327 267.2 Da LogP 0.84 TPSA 112.9 ✓ Ro5 ✓ Clean c1ccc(cc1)COC(=O)N[C@@H](CC(=O)O)C(=O)O
ORN RCSB PDB P0A6F1 132.2 Da LogP -0.86 TPSA 89.3 ✓ Ro5 ✓ Clean C(C[C@@H](C(=O)O)N)CN
Q5A RCSB PDB P31327 390.5 Da LogP 3.49 TPSA 65.5 ✓ Ro5 ✓ Clean Cc1csc(n1)NC(=O)C2CCN(CC2)C(=O)N(C)Cc3ccc(cc3)F
SU8 RCSB PDB P31327 174.2 Da LogP 1.35 TPSA 74.6 ✓ Ro5 ✓ Clean CCCC[C@H](CC(=O)O)C(=O)O
SUH RCSB PDB P31327 132.1 Da LogP 0.18 TPSA 74.6 ✓ Ro5 ✓ Clean C[C@@H](CC(=O)O)C(=O)O
WOC RCSB PDB P31327 146.1 Da LogP 0.57 TPSA 74.6 ✓ Ro5 ✓ Clean CC(C)(CC(=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.