KpATCC43816 Protein target profile
glutamate synthase (NADPH) large chain glutamatesynthase, large subunit
Accession: VK055_3853
Strong target candidate with converging metabolic, structural and chemical evidence.
Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.
Main supporting evidence
Evidence coverage
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
- 3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- Y
- DEG identity (%)
- 59.903 Higher values support similarity to known essential genes.
- DEG E-value
- 0.0 Smaller values mean stronger essential-gene similarity.
Structure confidence
- ColabFold pLDDT
- 94.65 0-100 confidence; >70 supports local structural interpretation.
Binding-site evidence
AlphaFold DB / UniProt modelP2Rank'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.
Sequence
Primary amino-acid sequence viewer.
MQHRGAILADGKTGDGCGLLLQKPDRFFRIVAEERGWRLAKNYAVGMLFLNKDPELAKAARRIVEEELQLETLSIVGWRDVPTNEGVLGEIALSSLPRIEQIFVNAPAGWRPRDMERRLFIARRRIEKRLQEDKDFYVCSLSNLVNIYKGLCMPADLPRFYLDLADLRLESAICLFHQRFSTNTVPRWPLAQPFRYLAHNGEINTITGNRQWARARTYKFQTPLIPDLHDAAPFVNETGSDSSSMDNMLELLLAGGMDIVRAMRLLVPPAWQNNPDMDPELRSFFDFNSMHMEPWDGPAGIVMSDGRYAACNLDRNGLRPARYVITKDKLITCASEVGIWDYQPDEVVEKGRVGPGELMVIDTRAGRILHSAETDDDLKSRHPYKEWMEKNVRRLVPFEDLPDEEVGSRQLDDDTLASYQKQFNYSAEELDSVLRVLGENGQEAVGSMGDDTPFAVLSSQPRIIYDYFRQQFAQVTNPPIDPLREAHVMSLATSIGREMNVFCEAEGQAHRLSFKSPILLYSDFKQLTTMEEEHYRADVLDITFNPAEASLSETVKALCDKAEQMVRDGTVLLVLSDRNIAKDRLPVPAPMAVGAIQTRLVDKSLRCDANIIVETASARDPHHFAVLLGFGATAIYPYLAYETLAKLVDSKAIDKPYRAVMLNYRNGINKGLYKIMSKMGISTIASYRCSKLFEAVGLHRDVSDLCFQGVVSRIGGASFDDFQQDLLNLSKRAWLARKPLAQGGLLKYVHGGEYHAYNPDVVRTLQQAVQSGEYSDYQQYAKLVNERPAATLRDLLALNPGEDAISIDEVEPAKELFKRFDTAAMSIGALSPEAHESLAEAMNSIGGFSNSGEGGEDPARYGTNKVSRIKQVASGRFGVTPAYLVNADVIQIKVAQGAKPGEGGQLPGDKVTPYIAKLRYSVPGVTLISPPPHHDIYSIEDLAQLIFDLKQVNPKAMISVKLVSEPGVGTIATGVAKAYADLITIAGYDGGTGASPLSSVKYAGCPWELGLVETQQALVANGLRHKIRLQVDGGLKTGLDIIKAAILGAESFGFGTGPMVALGCKYLRICHLNNCATGVATQDDKLRKNHYHGLPFKVTNYFEFIARETRELMAQLGVKRLVDLIGRTDLLKELDGFTAKQQKLDLGKLLETAEPHPGKALYCTENNPPFDNGVLNAQLLQQAKPYVDEKQSKTFWFDIRNTDRSVGASLSGYIAQTHGDQGLAGDPIVAHFSGTAGQSFGVWNAGGVELHLTGDANDYVGKGMAGGLLAIRPPVGSAFRSHEASIIGNTCLYGATGGRLYAAGRAGERFAVRNSGAITVVEGIGDNGCEYMTGGIVCVLGKTGVNFGAGMTGGFAYVLDEDGDFRKRVNPELVEVLDVDSLAIHEEHLRGLITEHVQLTGSQRGEEILANWPAFSAKFALVKPKSSDVKALLGHRSRSAAELRVQAQ
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Subcellular localization
- Localization
- Cytoplasmic
Enzyme Commission (EC)
1Gene Ontology (GO)
9- GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
- GO:0015930 Catalysis of the formation of L-glutamine and 2-oxoglutarate from L-glutamate, using NADH, NADPH or ferredoxin as hydrogen acceptors.
- GO:0006537 OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid.
- GO:0016638 Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
- GO:0006807 OBSOLETE. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
- GO:0051538 Binding to a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
- GO:0004355 Catalysis of the reaction: 2 L-glutamate + NADP+ = 2-oxoglutarate + L-glutamine + H+ + NADPH. This is a two-step reaction: (a) L-glutamate + NH4+ = L-glutamine + H2O, (b) L-glutamate + NADP+ + H2O = NH4+ + 2-oxoglutarate + NADPH + H+.
- GO:0046872 Binding to a metal ion.
- GO:0019676 The pathway by which ammonia is processed and incorporated into a cell. In an energy-rich (glucose-containing), nitrogen-poor environment, glutamine synthetase and glutamate synthase form an ammonia assimilatory cycle, in which ammonia is incorporated into L-glutamate to form L-glutamine, which then combines with alpha-ketoglutarate to regenerate L-glutamate. This ATP-dependent cycle is essential for nitrogen-limited growth and for steady-state growth with some sources of nitrogen.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 1 | 387 | Pfam | PF00310 | Glutamine amidotransferases class-II |
| 1 | 387 | InterPro | IPR017932 | Glutamine amidotransferase type 2 domain |
| 758 | 1132 | CDD | cd02808 | GltS_FMN |
| 758 | 1132 | InterPro | IPR002932 | Glutamate synthase domain |
| 746 | 1157 | FunFam | G3DSA:3.20.20.70:FF:000061 | Glutamate synthase large subunit |
| 1 | 391 | SUPERFAMILY | SSF56235 | N-terminal nucleophile aminohydrolases (Ntn hydrolases) |
| 1 | 391 | InterPro | IPR029055 | Nucleophile aminohydrolases, N-terminal |
| 1 | 506 | Gene3D | G3DSA:3.60.20.10 | Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 |
| 1 | 506 | InterPro | IPR029055 | Nucleophile aminohydrolases, N-terminal |
| 1159 | 1429 | Gene3D | G3DSA:2.160.20.60 | - |
| 1159 | 1429 | InterPro | IPR036485 | Glutamate synthase, alpha subunit, C-terminal domain superfamily |
| 1173 | 1427 | SUPERFAMILY | SSF69336 | Alpha subunit of glutamate synthase, C-terminal domain |
| 1173 | 1427 | InterPro | IPR036485 | Glutamate synthase, alpha subunit, C-terminal domain superfamily |
| 1161 | 1429 | FunFam | G3DSA:2.160.20.60:FF:000002 | Glutamate synthase, large subunit |
| 1198 | 1380 | Pfam | PF01493 | GXGXG motif |
| 1198 | 1380 | InterPro | IPR002489 | Glutamate synthase, alpha subunit, C-terminal |
| 419 | 699 | Pfam | PF04898 | Glutamate synthase central domain |
| 419 | 699 | InterPro | IPR006982 | Glutamate synthase, central-N |
| 396 | 1153 | SUPERFAMILY | SSF51395 | FMN-linked oxidoreductases |
| 755 | 1118 | Pfam | PF01645 | Conserved region in glutamate synthase |
| 755 | 1118 | InterPro | IPR002932 | Glutamate synthase domain |
| 391 | 747 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I |
| 391 | 747 | InterPro | IPR013785 | Aldolase-type TIM barrel |
| 444 | 1133 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I |
| 444 | 1133 | InterPro | IPR013785 | Aldolase-type TIM barrel |
| 5 | 1428 | PANTHER | PTHR11938 | FAD NADPH DEHYDROGENASE/OXIDOREDUCTASE |
| 1 | 364 | ProSiteProfiles | PS51278 | Glutamine amidotransferase type 2 domain profile. |
| 1 | 364 | InterPro | IPR017932 | Glutamine amidotransferase type 2 domain |
| 1 | 382 | CDD | cd00713 | GltS |
| 1 | 397 | FunFam | G3DSA:3.60.20.10:FF:000001 | Glutamate synthase, large subunit |
| 1175 | 1425 | CDD | cd00982 | gltB_C |
| 1175 | 1425 | InterPro | IPR002489 | Glutamate synthase, alpha subunit, C-terminal |
| 398 | 745 | FunFam | G3DSA:3.20.20.70:FF:000109 | Glutamate synthase, large subunit |
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.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
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- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
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Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
All structural evidence
Structural evidence
0 + 2Experimental 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_A0A0H3GY60
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_3853
|
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.
Structural ligand evidence is available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| AKG RCSB PDB | P55038 | 146.1 Da LogP -0.50 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
C(CC(=O)O)C(=O)C(=O)O
|
|
| F3S RCSB PDB | P55038 | 295.8 Da LogP 2.59 TPSA 0.0 | ✓ Ro5 | ✓ Clean |
S1[Fe]2S[Fe]3[S]2[Fe]1S3
|
|
| OMT RCSB PDB | Q05755 | 181.2 Da LogP -1.17 TPSA 97.5 | ✓ Ro5 | ✓ Clean |
CS(=O)(=O)CC[C@@H](C(=O)O)N
|
|
| ONL RCSB PDB | P55038 | 145.2 Da LogP -0.23 TPSA 80.4 | ✓ Ro5 | ✓ Clean |
CC(=O)CC[C@@H](C(=O)O)N
|
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC19429847 ZINC | 0.607 | 208.3 Da LogP -1.16 TPSA 80.5 | ✓ Ro5 | ✓ Clean |
CN(C)C(=O)[C@@H](N)CCS(C)(=O)=O
|
| ZINC19429848 ZINC | 0.607 | 208.3 Da LogP -1.16 TPSA 80.5 | ✓ Ro5 | ✓ Clean |
CN(C)C(=O)[C@H](N)CCS(C)(=O)=O
|
| ZINC26513844 ZINC | 0.607 | 209.3 Da LogP -0.69 TPSA 86.5 | ✓ Ro5 | ✓ Clean |
CCOC(=O)[C@@H](N)CCS(C)(=O)=O
|
| ZINC26513846 ZINC | 0.607 | 209.3 Da LogP -0.69 TPSA 86.5 | ✓ Ro5 | ✓ Clean |
CCOC(=O)[C@H](N)CCS(C)(=O)=O
|
| ZINC3055005 ZINC | 0.565 | 204.2 Da LogP -0.63 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O
|
| ZINC3055007 ZINC | 0.565 | 204.2 Da LogP -0.63 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC3055010 ZINC | 0.565 | 204.2 Da LogP -0.63 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC1555366 ZINC | 0.542 | 232.3 Da LogP 0.15 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCCCC[C@H](N)C(=O)O)C(=O)O
|
| ZINC1555367 ZINC | 0.542 | 232.3 Da LogP 0.15 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC1555369 ZINC | 0.542 | 232.3 Da LogP 0.15 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC1720127 ZINC | 0.542 | 218.3 Da LogP -0.24 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCCC[C@H](N)C(=O)O)C(=O)O
|
| ZINC1720128 ZINC | 0.542 | 218.3 Da LogP -0.24 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC1720130 ZINC | 0.542 | 218.3 Da LogP -0.24 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC1643467 ZINC | 0.517 | 217.2 Da LogP -1.12 TPSA 117.7 | ✓ Ro5 | ✓ Clean |
CS(=O)(=O)CC[C@@H](N)P(=O)(O)O
|
| ZINC6425006 ZINC | 0.517 | 217.2 Da LogP -1.12 TPSA 117.7 | ✓ Ro5 | ✓ Clean |
CS(=O)(=O)CC[C@H](N)P(=O)(O)O
|
| ZINC34050079 ZINC | 0.516 | 224.2 Da LogP -0.91 TPSA 130.0 | ✓ Ro5 | ✓ Clean |
CS(=O)(=O)/N=C(\O)CC[C@H](N)C(=O)O
|
| ZINC1570993 ZINC | 0.500 | 215.3 Da LogP 2.93 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCC[C@H](N)C(=O)O
|
| ZINC1570999 ZINC | 0.500 | 229.4 Da LogP 3.32 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCC[C@H](N)C(=O)O
|
| ZINC1620974 ZINC | 0.500 | 243.4 Da LogP 3.71 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCC[C@H](N)C(=O)O
|
| ZINC1742220 ZINC | 0.500 | 201.3 Da LogP 2.54 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCC[C@H](N)C(=O)O
|
| ZINC2035155 ZINC | 0.500 | 215.3 Da LogP 2.93 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCC[C@@H](N)C(=O)O
|
| ZINC2035157 ZINC | 0.500 | 201.3 Da LogP 2.54 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCC[C@@H](N)C(=O)O
|
| ZINC2037129 ZINC | 0.500 | 243.4 Da LogP 3.71 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCC[C@@H](N)C(=O)O
|
| ZINC43531622 ZINC | 0.500 | 271.4 Da LogP 4.49 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCCC[C@H](N)C(=O)O
|
| ZINC43531626 ZINC | 0.500 | 271.4 Da LogP 4.49 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCCC[C@@H](N)C(=O)O
|
| ZINC8437446 ZINC | 0.500 | 229.4 Da LogP 3.32 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCC[C@@H](N)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.