Protein target profile

VK055_4666

guaA GMP synthetase

Genome: KpATCC43816 Gene: AIK83200.1 guaA 3D evidence: AlphaFold DB model + ColabFold model Metabolism 3 reactions UniProt A0A0H3GRL9
Length 525
Pocket druggability 0.019
Metabolic reactions 3
Chokepoint No
Direct ligand evidence 0 53 total records
Functional annotation 0 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
Hit
Human identity (%)
36.477 Lower values reduce human off-target concern.
Human E-value
2.23e-93
Gut microbiome similarity
47.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
96.19 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
91.84 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 0.019
Structure A0A0H3GRL9
Pocket Pocket 25
P2Rank 0.918
Structure A0A0H3GRL9
Pocket Pocket 1
ColabFold model
FPocket 0.518 · Pocket 2
P2Rank 0.904 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 2241 / 4744 genomes with a hit
Prevalence 47.2%

Cross-references

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

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 91.4% of genes in this genome.

Relative network centrality 91.4% more central than 91.4% of genes in this genome
Chokepoint Not a chokepoint
Catalyzed reactions

3 reactions 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.

MTENIHKHRILILDFGSQYTQLVARRVRELGVYCELWAWDVTEAQIREFNPSGIILSGGPESTTEENSPRAPQYVFEAGVPVFGVCYGMQTMAMQLGGHVEGSNEREFGYAQVEVVNDSALVRGIEDSLTADGKPLLDVWMSHGDKVTAIPADFVTVASTDNCPFAIMANEEKRFYGVQFHPEVTHTRQGMRMLERFVRDICQCEALWTPAKIIDDAVERIRQQVGDDKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRLNEAQQVMEMFGDHFGLNIVHVEGEQRFLDALAGESDPEAKRKIIGRVFVEVFDEEALKLDDVKWLAQGTIYPDVIESAASATGKAHVIKSHHNVGGLPKEMKMGLVEPLRELFKDEVRKIGLELGLPYDMLYRHPFPGPGLGVRVLGEVKKEYCDLLRRADAIFIEELHKADLYNKVSQAFTVFLPVRSVGVMGDGRKYDWVVSLRAVETIDFMTAHWAHLPYDFLGRVSNRIINEVNGISRVVYDISGKPPATIEWE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0003921 Catalysis of the reaction: ATP + XMP + NH4+ = AMP + diphosphate + GMP + 2H+.
  • GO:0006177 The chemical reactions and pathways resulting in the formation of GMP, guanosine monophosphate.
  • GO:0006164 The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
  • GO:0003922 Catalysis of the reaction: ATP + XMP + L-glutamine + H2O = AMP + diphosphate + GMP + L-glutamate + 2H+.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

41 records
Show feature table
Start End DB Term Name
9 207 ProSiteProfiles PS51273 Glutamine amidotransferase type 1 domain profile.
12 199 Pfam PF00117 Glutamine amidotransferase class-I
12 199 InterPro IPR017926 Glutamine amidotransferase
209 410 FunFam G3DSA:3.40.50.620:FF:000001 GMP synthase [glutamine-hydrolyzing]
209 410 Gene3D G3DSA:3.40.50.620 HUPs
209 410 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
411 525 FunFam G3DSA:3.30.300.10:FF:000002 GMP synthase [glutamine-hydrolyzing]
212 525 NCBIfam TIGR00884 glutamine-hydrolyzing GMP synthase, C-terminal domain
212 525 InterPro IPR001674 GMP synthase, C-terminal
10 525 PANTHER PTHR11922 GMP SYNTHASE-RELATED
177 190 PRINTS PR00096 Glutamine amidotransferase superfamily signature
54 63 PRINTS PR00096 Glutamine amidotransferase superfamily signature
81 92 PRINTS PR00096 Glutamine amidotransferase superfamily signature
217 258 Pfam PF02540 NAD synthase
217 258 InterPro IPR022310 NAD/GMP synthase
197 420 SUPERFAMILY SSF52402 Adenine nucleotide alpha hydrolases-like
5 204 SUPERFAMILY SSF52317 Class I glutamine amidotransferase-like
5 204 InterPro IPR029062 Class I glutamine amidotransferase-like
405 525 SUPERFAMILY SSF54810 GMP synthetase C-terminal dimerisation domain
433 524 Pfam PF00958 GMP synthase C terminal domain
433 524 InterPro IPR001674 GMP synthase, C-terminal
9 206 Gene3D G3DSA:3.40.50.880 -
9 206 InterPro IPR029062 Class I glutamine amidotransferase-like
411 525 Gene3D G3DSA:3.30.300.10 -
7 206 FunFam G3DSA:3.40.50.880:FF:000001 GMP synthase [glutamine-hydrolyzing]
10 198 CDD cd01742 GATase1_GMP_Synthase
10 198 InterPro IPR004739 GMP synthase, glutamine amidotransferase
7 525 Hamap MF_00344 GMP synthase [glutamine-hydrolyzing] [guaA].
7 525 InterPro IPR022955 GMP synthase
51 65 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature
10 24 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature
81 97 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature
10 205 NCBIfam TIGR00888 glutamine-hydrolyzing GMP synthase, N-terminal domain
10 205 InterPro IPR004739 GMP synthase, glutamine amidotransferase
229 524 CDD cd01997 GMP_synthase_C
229 524 InterPro IPR001674 GMP synthase, C-terminal
208 400 ProSiteProfiles PS51553 GMP synthetase ATP pyrophosphatase (GMPS ATP-PPase) domain profile.
208 400 InterPro IPR025777 GMP synthetase ATP pyrophosphatase domain
81 92 PRINTS PR00097 Anthranilate synthase component II signature
54 63 PRINTS PR00097 Anthranilate synthase component II signature
177 190 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.

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

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

Site 1 P2Rank #1
0.918
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.238
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.157
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.102
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.067
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:181-181
UniProt: Active site:183-183
UniProt: Active site:86-86 Nucleophile
UniProt: Binding site:235-241
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_A0A0H3GRL9
AlphaFold DB full sequence Viewing
ColabFold VK055_4666
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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
MLA PDB via homolog 104.1 Da · LogP -0.45 · TPSA 74.6 Open detail RCSB PDB
POP PDB via homolog Detail RCSB PDB
XMP PDB via homolog Detail RCSB PDB
ZINC1532902 ZINC proposed compound · Tanimoto 0.700 Detail ZINC
ZINC2018106 ZINC proposed compound · Tanimoto 0.700 Detail ZINC

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
MLA RCSB PDB Q58531 104.1 Da LogP -0.45 TPSA 74.6 ✓ Ro5 ✓ Clean C(C(=O)O)C(=O)O
POP RCSB PDB P04079 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
XMP RCSB PDB P49915 365.2 Da LogP -3.44 TPSA 201.2 1 viol. ✓ Clean c1[nH+]c2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=…

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.