KpKP13 Protein target profile

Glutamate synthase [NADPH] small chain

Accession: KP13_03218

Gene: AHE42458.1 gltD 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GW91

Export view

Length 472

Pocket druggability (P2Rank · AlphaFold DB model) 0.954

Direct ligand evidence 0 33 total records

Functional annotation 1 EC 6 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.

Main supporting evidence

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.95, FPocket 0.77). Use the 3D pocket comparison to verify whether they identify the same site. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.77. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.95. Review the complete evidence below

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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 (%): 30.625 Lower values reduce human off-target concern.
Human E-value: 4.1e-08
Gut microbiome similarity: 3.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 68.23 Higher values support similarity to known essential genes.
DEG E-value: 0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 95.41 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) 0.954

Structure A0A0H3GW91

Pocket Pocket 1

Druggability (FPocket) 0.767

Structure A0A0H3GW91

Pocket Pocket 1

ColabFold model

P2Rank 0.947 · Pocket 1

FPocket 0.994 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 153 / 4744 genomes with a hit

Prevalence 3.2%

Sequence

Primary amino-acid sequence viewer.

MSQNVYQFIDLQRVDPPKKPLKIRKIEFVEIYEPFSEGQAKAQADRCLSCGNPYCEWKCPVHNYIPNWLKLANEGRIFEAAELSHQTNTLPEVCGRVCPQDRLCEGSCTLNDEFGAVTIGNIERYINDKAFEMGWRPDLSDVKPTGKTVAIIGAGPAGLACADVLTRNGVKAVVFDRHPEIGGLLTFGIPAFKLEKEVMTRRREIFTGMGIEFKLNTEVGRDVQLDDLLKEYDAVFLGVGTYQSMRGGLDNEDAPGVYDALPFLIANTKQIMGFGETADEPYVSMEGKRVVVLGGGDTAMDCVRTSVRQNAAHVICAYRRDEENMPGSKREVKNAREEGVEFQFNVQPLGVEVNANGKVCGVKMARTEMGQPDAKGRRRAEIVPGSEHVVPADAVVMAFGFRPHSMEWLAKHSVELDSQGRIIAPEGSENAFQTSNPKIFAGGDIVRGSDLVVTAIAEGRKAADGILNYLEV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

1.4.1.13

Gene Ontology (GO)

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:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
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:0006537 OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

28 records

Show feature table

Start	End	DB	Term	Name
25	134	Pfam	PF14691	Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
25	134	InterPro	IPR028261	Dihydroprymidine dehydrogenase domain II
145	269	Gene3D	G3DSA:3.50.50.60	-
145	269	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
318	338	Coils	Coil	Coil
374	470	Gene3D	G3DSA:3.50.50.60	-
374	470	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
10	144	Gene3D	G3DSA:1.10.1060.10	-
10	144	InterPro	IPR009051	Alpha-helical ferredoxin
324	337	PRINTS	PR00419	Adrenodoxin reductase family signature
148	170	PRINTS	PR00419	Adrenodoxin reductase family signature
171	184	PRINTS	PR00419	Adrenodoxin reductase family signature
290	304	PRINTS	PR00419	Adrenodoxin reductase family signature
213	223	PRINTS	PR00419	Adrenodoxin reductase family signature
38	69	ProSiteProfiles	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
38	69	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
146	267	FunFam	G3DSA:3.50.50.60:FF:000077	Glutamate synthase small subunit
7	157	SUPERFAMILY	SSF46548	alpha-helical ferredoxin
145	401	SUPERFAMILY	SSF51971	Nucleotide-binding domain
148	459	Pfam	PF07992	Pyridine nucleotide-disulphide oxidoreductase
148	459	InterPro	IPR023753	FAD/NAD(P)-binding domain
276	373	Gene3D	G3DSA:3.50.50.60	-
276	373	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
285	472	FunFam	G3DSA:3.50.50.60:FF:000068	Glutamate synthase small subunit
9	145	FunFam	G3DSA:1.10.1060.10:FF:000004	Glutamate synthase, small subunit
6	472	NCBIfam	TIGR01318	glutamate synthase, small subunit
6	472	InterPro	IPR006006	Glutamate synthase NADPH small chain-like
3	471	PANTHER	PTHR42783	GLUTAMATE SYNTHASE [NADPH] SMALL CHAIN

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

0.954

Show in viewer

Surrounding area

Pocket 2 P2Rank #2

0.221

Show in viewer

Surrounding area

Pocket 3 P2Rank #3

0.219

Show in viewer

Surrounding area

Pocket 4 P2Rank #4

0.218

Show in viewer

Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1

0.767 Unusual size

Show in viewer

Surrounding area

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.947

Likely same site as FPocket 1 6.5 Å 39 shared residues 74% of smaller site

Show in viewer

Surrounding area

Pocket 2 P2Rank #2

0.244

Show in viewer

Surrounding area

Pocket 3 P2Rank #3

0.223

Show in viewer

Surrounding area

Pocket 4 P2Rank #4

0.099

Show in viewer

Surrounding area

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_A0A0H3GW91	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_03218	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.

33 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 5 records from similar proteins

Structural ligands 5 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 28 similarity-based ZINC candidates

Best available ligand signal

AKG PDB via homolog 146.1 Da · LogP -0.50 · TPSA 91.7 Open detail RCSB PDB

F3S PDB via homolog Detail RCSB PDB

FES PDB via homolog Detail RCSB PDB

MDE PDB via homolog Detail RCSB PDB

OMT PDB via homolog Detail RCSB PDB

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	2VDC	Q05756	146.1 Da LogP -0.50 TPSA 91.7	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)C(=O)O`
F3S RCSB PDB	2VDC	Q05756	295.8 Da LogP 2.59 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]2S[Fe]3[S]2[Fe]1S3`
FES RCSB PDB	5VJ7	I6V148	175.8 Da LogP 1.29 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]S[Fe]1`
MDE RCSB PDB	1PS9	P42593	994.9 Da LogP 0.91 TPSA 382.6	3 viol.	✓ Clean	`CCCCC[C@@H](C\C=C\C(=O)SCCNC(=O)CCNC(C(=O)C(C)(…`
OMT RCSB PDB	2VDC	Q05756	181.2 Da LogP -1.17 TPSA 97.5	✓ Ro5	✓ Clean	`CS(=O)(=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`
ZINC13537595 ZINC	0.567	208.3 Da LogP 0.25 TPSA 104.2	✓ Ro5	✓ Clean	`CCC[S@](=N)(=O)CC[C@H](N)C(=O)O`
ZINC1579929 ZINC	0.567	208.3 Da LogP 0.25 TPSA 104.2	✓ Ro5	✓ Clean	`CCC[S@@](=N)(=O)CC[C@@H](N)C(=O)O`
ZINC1607787 ZINC	0.567	223.3 Da LogP 0.00 TPSA 97.5	✓ Ro5	✓ Clean	`CCCCS(=O)(=O)CC[C@@H](N)C(=O)O`
ZINC17130070 ZINC	0.567	208.3 Da LogP 0.25 TPSA 104.2	✓ Ro5	✓ Clean	`CCC[S@](=N)(=O)CC[C@@H](N)C(=O)O`
ZINC3651794 ZINC	0.567	208.3 Da LogP 0.25 TPSA 104.2	✓ Ro5	✓ Clean	`CCC[S@@](=N)(=O)CC[C@H](N)C(=O)O`
ZINC5784111 ZINC	0.567	223.3 Da LogP 0.00 TPSA 97.5	✓ Ro5	✓ Clean	`CCCCS(=O)(=O)CC[C@H](N)C(=O)O`
ZINC34050079 ZINC	0.548	224.2 Da LogP -0.91 TPSA 130.0	✓ Ro5	✓ Clean	`CS(=O)(=O)/N=C(\O)CC[C@H](N)C(=O)O`
ZINC3055005 ZINC	0.542	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	0.542	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	0.542	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC12405097 ZINC	0.531	222.3 Da LogP 0.64 TPSA 104.2	✓ Ro5	✓ Clean	`CCCC[S@@](=N)(=O)CC[C@H](N)C(=O)O`
ZINC12405142 ZINC	0.531	222.3 Da LogP 0.64 TPSA 104.2	✓ Ro5	✓ Clean	`CCCC[S@](=N)(=O)CC[C@@H](N)C(=O)O`
ZINC1529986 ZINC	0.531	222.3 Da LogP 0.64 TPSA 104.2	✓ Ro5	✓ Clean	`CCCC[S@](=N)(=O)CC[C@H](N)C(=O)O`
ZINC1529987 ZINC	0.531	222.3 Da LogP 0.64 TPSA 104.2	✓ Ro5	✓ Clean	`CCCC[S@@](=N)(=O)CC[C@@H](N)C(=O)O`
ZINC379592171 ZINC	0.531	224.3 Da LogP -0.88 TPSA 109.5	✓ Ro5	✓ Clean	`CCCNS(=O)(=O)CC[C@H](N)C(=O)O`
ZINC379592172 ZINC	0.531	224.3 Da LogP -0.88 TPSA 109.5	✓ Ro5	✓ Clean	`CCCNS(=O)(=O)CC[C@@H](N)C(=O)O`
ZINC1555366 ZINC	0.520	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	0.520	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	0.520	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	0.520	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	0.520	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	0.520	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`

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.

Sequence

UniProt A0A0H3GW91