Protein target profile

VK055_1235

succinylglutamic semialdehyde dehydrogenase

Genome: KpATCC43816 Gene: astD2 AIK79858.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GN76

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Length 492

Pocket druggability 0.901

Metabolic reactions 1

Chokepoint Yes

Direct ligand evidence 0 35 total records

Functional annotation 1 EC 6 GO

Target summary

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

Metabolic bottleneck Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Central metabolic position More central than 93.5% of genes in this genome. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.94. Review the complete evidence below

Risks to review

Evidence coverage

Core evidence streams are available for this target.

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 (%): 34.409 Lower values reduce human off-target concern.
Human E-value: 1.49e-06
Gut microbiome similarity: 2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 57.26 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: 96.87 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 0.901

Structure A0A0H3GN76

Pocket Pocket 7

P2Rank 0.938

Structure A0A0H3GN76

Pocket Pocket 1

ColabFold model

FPocket 0.595 · Pocket 4

P2Rank 0.911 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 115 / 4744 genomes with a hit

Prevalence 2.4%

Cross-references

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

Sequence

UniProt A0A0H3GN76

Pathways

KEGG R05049 BioCyc SUCCGLUALDDEHYD-RXN

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a producing chokepoint reaction in Arginine and proline metabolism, more central than 93.5% of genes in this genome.

Relative network centrality 93.5% more central than 93.5% of genes in this genome

Chokepoint Chokepoint gene

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSLWINGEWRPGRGPGFSKQDPVNLKVVWQGEAADAGQVAEAVAAARQAFPSWARLPFAARQAIVEKFAALLEASKAELTAVIGAETGKPRWEAAGEVTAMINKVAISVKAYHVRTGEQHSDLPDGAATLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPRSGEAVVKLWQQAGLPAGVLNLVQGGRETGEALSGQADIDGLLFTGSSTTGFHLHRQLAGQPQKILALEMGGNNPLIVDDPRDVDAAVHLTIQSAFITAGQRCTCARRLLVRRGEAGDVFLSRLVTVSQRLIPAAWDAEPQPFLGGLISEQAAQKVHQAWLQRVAAGAVTLLEPRLLQAGTSLLTPGIVDMSNVAKVEDEEVFGPLLGVWRYDTFEEGIALANATRFGLSCGLISPEREKFERLLLEARAGIVNWNKPLTGAASTAPFGGTGASGNHRPGAWYAADYCAWPMASLESPTLTLPASLSPGLDFLAGEAS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1.2.1.71

Gene Ontology (GO)

GO:0043824 Catalysis of the reaction: N-succinyl-L-glutamate 5-semialdehyde + H2O + NAD+ = N-succinyl-L-glutamate + 2 H+ + NADH.
GO:0016620 Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
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:0006527 The chemical reactions and pathways resulting in the breakdown of L-arginine.
GO:0019544 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-arginine into other compounds, including L-glutamate.
GO:0019545 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-arginine into other compounds, including succinate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
247	437	FunFam	G3DSA:3.40.309.10:FF:000013	N-succinylglutamate 5-semialdehyde dehydrogenase
2	455	SUPERFAMILY	SSF53720	ALDH-like
2	455	InterPro	IPR016161	Aldehyde/histidinol dehydrogenase
242	249	ProSitePatterns	PS00687	Aldehyde dehydrogenases glutamic acid active site.
242	249	InterPro	IPR029510	Aldehyde dehydrogenase, glutamic acid active site
7	449	Gene3D	G3DSA:3.40.605.10	Aldehyde Dehydrogenase; Chain A, domain 1
7	449	InterPro	IPR016162	Aldehyde dehydrogenase, N-terminal
3	486	NCBIfam	TIGR03240	succinylglutamate-semialdehyde dehydrogenase
3	486	InterPro	IPR017649	Succinylglutamate-semialdehyde dehydrogenase
270	281	ProSitePatterns	PS00070	Aldehyde dehydrogenases cysteine active site.
270	281	InterPro	IPR016160	Aldehyde dehydrogenase, cysteine active site
11	458	Pfam	PF00171	Aldehyde dehydrogenase family
11	458	InterPro	IPR015590	Aldehyde dehydrogenase domain
247	437	Gene3D	G3DSA:3.40.309.10	Aldehyde Dehydrogenase; Chain A, domain 2
247	437	InterPro	IPR016163	Aldehyde dehydrogenase, C-terminal
1	486	Hamap	MF_01174	N-succinylglutamate 5-semialdehyde dehydrogenase [astD].
1	486	InterPro	IPR017649	Succinylglutamate-semialdehyde dehydrogenase
50	469	CDD	cd07095	ALDH_SGSD_AstD
50	469	InterPro	IPR017649	Succinylglutamate-semialdehyde dehydrogenase
7	251	FunFam	G3DSA:3.40.605.10:FF:000010	N-succinylglutamate 5-semialdehyde dehydrogenase
3	458	PANTHER	PTHR11699	ALDEHYDE DEHYDROGENASE-RELATED

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 #7

0.901

Likely same site as P2Rank 1 0.4 Å 22 shared residues 96% of smaller site

Unusual size

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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

0.938

Likely same site as FPocket 7 0.4 Å 22 shared residues 96% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.774

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Surrounding area

Site 3 P2Rank #3

0.12

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Surrounding area

Site 4 P2Rank #4

0.05

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Surrounding area

Site 5 P2Rank #5

0.026

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Surrounding area

Residue sets

UniProt: Active site:243-243

UniProt: Active site:277-277

UniProt: Binding site:220-225

Binding pockets · FPocket

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

Site 1 FPocket #4

0.595

Likely same site as P2Rank 1 1.9 Å 17 shared residues 85% of smaller site

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Surrounding area

Site 2 FPocket #3

0.247

Likely same site as P2Rank 2 2.7 Å 23 shared residues 85% of smaller site

Unusual size

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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

0.911

Likely same site as FPocket 4 1.9 Å 17 shared residues 85% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.857

Likely same site as FPocket 3 2.7 Å 23 shared residues 85% of smaller site

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Surrounding area

Site 3 P2Rank #3

0.067

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Surrounding area

Site 4 P2Rank #4

0.029

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Surrounding area

Site 5 P2Rank #5

0.025

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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_A0A0H3GN76	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_1235	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.

35 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 9 records from similar proteins

Structural ligands 9 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 26 similarity-based ZINC candidates

Best available ligand signal

2VS PDB via homolog 142.1 Da · LogP 0.27 · TPSA 74.6 Open detail RCSB PDB

5OZ PDB via homolog Detail RCSB PDB

6OA PDB via homolog Detail RCSB PDB

6OD PDB via homolog Detail RCSB PDB

6OH 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
2VS RCSB PDB	4NPI	Q83V33	142.1 Da LogP 0.27 TPSA 74.6	✓ Ro5	✓ Clean	`C(=C/C=O)\C=C(\C(=O)O)/O`
5OZ RCSB PDB	5EK6	G7VCG0	72.1 Da LogP 0.84 TPSA 17.1	✓ Ro5	✓ Clean	`CC(C)C=O`
6OA RCSB PDB	4OU2	Q83V33	144.1 Da LogP 0.06 TPSA 77.8	✓ Ro5	✓ Clean	`C(/C=C/C=C(/C(=O)O)\O)O`
6OD RCSB PDB	4I25	Q83V33	141.1 Da LogP -0.33 TPSA 80.4	✓ Ro5	✓ Clean	`C(=C/C=O)\C=C(/C(=O)O)\N`
6OH RCSB PDB	4I2R	Q83V33	142.1 Da LogP 0.27 TPSA 74.6	✓ Ro5	✓ Clean	`C(=C/C=O)\C=C(/C(=O)O)\O`
6UN RCSB PDB	5KLL	Q83V33	142.1 Da LogP 0.27 TPSA 74.6	✓ Ro5	✓ Clean	`C(=C/C(=O)C(=O)O)\C=C\O`
8YP RCSB PDB	5U0L	A1U5W8	156.3 Da LogP 3.33 TPSA 17.1	✓ Ro5	✓ Clean	`CCCCCCCCCC=O`
PPI RCSB PDB	6FK3	Q72KD3	74.1 Da LogP 0.48 TPSA 37.3	✓ Ro5	✓ Clean	`CCC(=O)O`
SIN RCSB PDB	3JU8	O50174	118.1 Da LogP -0.06 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)O`

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
ZINC1693894 ZINC	1.000	212.4 Da LogP 4.89 TPSA 17.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC=O`
ZINC43061660 ZINC	0.842	210.4 Da LogP 4.66 TPSA 17.1	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCC=O`
ZINC43061664 ZINC	0.842	210.4 Da LogP 4.66 TPSA 17.1	✓ Ro5	✓ Clean	`CCCCCC/C=C/CCCCCC=O`
ZINC13546064 ZINC	0.750	210.4 Da LogP 4.66 TPSA 17.1	✓ Ro5	✓ Clean	`CCCC/C=C\CCCCCCCC=O`
ZINC1850393 ZINC	0.750	210.4 Da LogP 4.66 TPSA 17.1	✓ Ro5	✓ Clean	`CCCC/C=C/CCCCCCCC=O`
ZINC1532902 ZINC	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106 ZINC	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC3593496 ZINC	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497 ZINC	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC14686440 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC2569627 ZINC	0.591	210.4 Da LogP 4.66 TPSA 17.1	✓ Ro5	✓ Clean	`CC/C=C/CCCCCCCCCC=O`
ZINC33949609 ZINC	0.591	210.4 Da LogP 4.66 TPSA 17.1	✓ Ro5	✓ Clean	`CC/C=C\CCCCCCCCCC=O`
ZINC13398039 ZINC	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC2528012 ZINC	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC1685772 ZINC	0.545	213.4 Da LogP 3.65 TPSA 29.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC=O`
ZINC59498852 ZINC	0.545	241.4 Da LogP 4.43 TPSA 29.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCNC=O`
ZINC35465466 ZINC	0.529	244.3 Da LogP 2.24 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCC(=O)CCC(=O)O`
ZINC39208104 ZINC	0.529	262.2 Da LogP -0.20 TPSA 127.2	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)OCCOC(=O)CCC(=O)O`
ZINC13398014 ZINC	0.522	220.2 Da LogP -1.07 TPSA 110.1	✓ Ro5	✓ Clean	`COC(=O)CC(O)(CC(=O)OC)C(=O)O`
ZINC33606582 ZINC	0.522	212.4 Da LogP 4.74 TPSA 17.1	✓ Ro5	✓ Clean	`CC(C)CCCCCCCCCCC=O`
ZINC100969993 ZINC	0.500	359.5 Da LogP 2.70 TPSA 123.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC100969996 ZINC	0.500	359.5 Da LogP 2.70 TPSA 123.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC38682833 ZINC	0.500	286.3 Da LogP -0.61 TPSA 115.2	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)N1CCN(C(=O)CCC(=O)O)CC1`
ZINC4181831 ZINC	0.500	232.2 Da LogP -0.01 TPSA 129.0	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)C(CC(=O)O)CC(=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.