Protein target profile

KP13_02907

Succinate-semialdehyde dehydrogenase [NADP+]

Genome: KpKP13 Gene: AHE46184.1 gabD 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GIS3
Length 482
Pocket druggability 0.917
Direct ligand evidence 0 66 total records
Functional annotation 0 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.

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 (%)
56.485 Lower values reduce human off-target concern.
Human E-value
0.0
Gut microbiome similarity
4.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
67.5 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
98.48 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 0.917
Structure A0A0H3GIS3
Pocket Pocket 1
P2Rank 0.832
Structure A0A0H3GIS3
Pocket Pocket 1
ColabFold model
FPocket 0.902 · Pocket 1
P2Rank 0.85 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 230 / 4744 genomes with a hit
Prevalence 4.8%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MQLNDMTLFRQQAMIDGQWRDAPNGDVIAVTNPANGEQLGSVPKMGADETREAIEAANRALPAWRALTAKERANILRRWFDLMMENQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGKRIYGDTIPGHQADKRLLVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSALALAELANRAGIPAGVFNVVTGSAGAVGGELTSNPLVRKLSFTGSTEIGRQLMEQCAKNIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGVYDRFAEKLQQAVEKLRIGDGLQDGVTTGPLIDEKAVAKVEEHIADAIAKGAKVVTGGKPHALGGNFFQPTILVNVPDSAKVAKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYARDLSRVFRVGEALEYGIIGINTGIISTEVAPFGGVKASGLGREGSKYGIEDYLEIKYMCIGL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • 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:0009450 The chemical reactions and pathways resulting in the breakdown of gamma-aminobutyric acid (GABA).
  • GO:0009013 Catalysis of the reaction: succinate semialdehyde + NAD(P)+ + H2O = succinate + NAD(P)H + H+.
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0004777 Catalysis of the reaction: succinate semialdehyde + NAD+ + H2O = succinate + NADH + H+.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
258 447 FunFam G3DSA:3.40.309.10:FF:000004 Succinate-semialdehyde dehydrogenase I
19 477 Pfam PF00171 Aldehyde dehydrogenase family
19 477 InterPro IPR015590 Aldehyde dehydrogenase domain
6 481 PANTHER PTHR43353 SUCCINATE-SEMIALDEHYDE DEHYDROGENASE, MITOCHONDRIAL
5 481 SUPERFAMILY SSF53720 ALDH-like
5 481 InterPro IPR016161 Aldehyde/histidinol dehydrogenase
30 480 CDD cd07103 ALDH_F5_SSADH_GabD
25 276 FunFam G3DSA:3.40.605.10:FF:000005 Succinate-semialdehyde dehydrogenase I
254 261 ProSitePatterns PS00687 Aldehyde dehydrogenases glutamic acid active site.
254 261 InterPro IPR029510 Aldehyde dehydrogenase, glutamic acid active site
30 476 NCBIfam TIGR01780 succinate-semialdehyde dehydrogenase
30 476 InterPro IPR010102 Succinate semialdehyde dehydrogenase
258 447 Gene3D G3DSA:3.40.309.10 Aldehyde Dehydrogenase; Chain A, domain 2
258 447 InterPro IPR016163 Aldehyde dehydrogenase, C-terminal
282 293 ProSitePatterns PS00070 Aldehyde dehydrogenases cysteine active site.
282 293 InterPro IPR016160 Aldehyde dehydrogenase, cysteine active site
25 472 Gene3D G3DSA:3.40.605.10 Aldehyde Dehydrogenase; Chain A, domain 1
25 472 InterPro IPR016162 Aldehyde dehydrogenase, N-terminal

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 #1
0.917
Likely same site as P2Rank 2 1.2 Å 12 shared residues 100% 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
0.832
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Surrounding area
Site 2 P2Rank #2
0.632
Likely same site as FPocket 1 1.2 Å 12 shared residues 100% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.0
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Surrounding area
Residue sets
UniProt: Active site:255-255
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_A0A0H3GIS3
AlphaFold DB full sequence Viewing
ColabFold KP13_02907
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.

66 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 16 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 8 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
0D8 PDB via homolog 75.1 Da · LogP -0.67 · TPSA 46.2 Open detail RCSB PDB
AE3 PDB via homolog Detail RCSB PDB
CHT PDB via homolog Detail RCSB PDB
DXC PDB via homolog Detail RCSB PDB
ETX 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
0D8 RCSB PDB P17202 75.1 Da LogP -0.67 TPSA 46.2 ✓ Ro5 ✓ Clean C(CN)CO
AE3 RCSB PDB P17202 134.2 Da LogP 0.03 TPSA 38.7 ✓ Ro5 ✓ Clean CCOCCOCCO
CHT RCSB PDB P17202 104.2 Da LogP -0.32 TPSA 20.2 ✓ Ro5 ✓ Clean C[N+](C)(C)CCO
DXC RCSB PDB P25553 392.6 Da LogP 4.48 TPSA 77.8 ✓ Ro5 ✓ Clean C[C@H](CCC(=O)O)[C@H]1CC[C@@H]2[C@@]1([C@H](C[C…
ETX RCSB PDB P17202 90.1 Da LogP 0.02 TPSA 29.5 ✓ Ro5 ✓ Clean CCOCCO
LAC RCSB PDB P25553 90.1 Da LogP -0.55 TPSA 57.5 ✓ Ro5 ✓ Clean C[C@H](C(=O)O)O
SIN RCSB PDB P51649 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
TAP RCSB PDB P28037 759.5 Da LogP -3.00 TPSA 350.6 3 viol. ✓ Clean c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P…

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.