Protein target profile

KP13_03893

Succinate-semialdehyde dehydrogenase [NADP+]

Genome: KpKP13 Gene: AHE45362.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GMI2
Length 482
Pocket druggability 0.933
Direct ligand evidence 0 165 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 (%)
53.556 Lower values reduce human off-target concern.
Human E-value
2.8399999999999998e-176
Gut microbiome similarity
4.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
61.311 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
97.87 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 0.933
Structure A0A0H3GMI2
Pocket Pocket 1
P2Rank 0.852
Structure A0A0H3GMI2
Pocket Pocket 1
ColabFold model
FPocket 0.985 · Pocket 1
P2Rank 0.727 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 215 / 4744 genomes with a hit
Prevalence 4.5%

Cross-references

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

Chemistry

ChEMBL CHEMBL3660752 ChEMBL CHEMBL113123 ChEMBL CHEMBL112696 ChEMBL CHEMBL3660748 ChEMBL CHEMBL3660728 ChEMBL CHEMBL3660742 ChEMBL CHEMBL3660747 ChEMBL CHEMBL3660751 ChEMBL CHEMBL3660739 ChEMBL CHEMBL3660744 ChEMBL CHEMBL3660749 ChEMBL CHEMBL3660730 ChEMBL CHEMBL3660732 ChEMBL CHEMBL3660738 ChEMBL CHEMBL112007 ChEMBL CHEMBL113640 ChEMBL CHEMBL3660726 ChEMBL CHEMBL3660727 ChEMBL CHEMBL3660735 ChEMBL CHEMBL3660731 ChEMBL CHEMBL3660741 ChEMBL CHEMBL3660745 ChEMBL CHEMBL3660743 ChEMBL CHEMBL3660722 ChEMBL CHEMBL3667538 ChEMBL CHEMBL3667541 ChEMBL CHEMBL3667547 ChEMBL CHEMBL3660746 ChEMBL CHEMBL4072941 ChEMBL CHEMBL114083 ChEMBL CHEMBL114397 ChEMBL CHEMBL115092 ChEMBL CHEMBL486422 ChEMBL CHEMBL3660736 ChEMBL CHEMBL3660716 ChEMBL CHEMBL3128207 ChEMBL CHEMBL3660712 ChEMBL CHEMBL3660721 ChEMBL CHEMBL3667535 ChEMBL CHEMBL3660740 ChEMBL CHEMBL1349972 ChEMBL CHEMBL4090473 ChEMBL CHEMBL113113 ChEMBL CHEMBL115109 ChEMBL CHEMBL3660725 ChEMBL CHEMBL3660719 ChEMBL CHEMBL3660723 ChEMBL CHEMBL3660733 ChEMBL CHEMBL109641 ChEMBL CHEMBL113586 ChEMBL CHEMBL132065 ChEMBL CHEMBL3128203 ChEMBL CHEMBL3667536 ChEMBL CHEMBL3915386 ChEMBL CHEMBL113058 ChEMBL CHEMBL262662 ChEMBL CHEMBL326803 ChEMBL CHEMBL109649 ChEMBL CHEMBL111984 ChEMBL CHEMBL4078971 ChEMBL CHEMBL4081886 ChEMBL CHEMBL3660724 ChEMBL CHEMBL3667539 ChEMBL CHEMBL3667548 ChEMBL CHEMBL3660729 ChEMBL CHEMBL112165 ChEMBL CHEMBL3667537 ChEMBL CW2 ChEMBL CHEMBL112865 ChEMBL CHEMBL109868 ChEMBL CHEMBL115314 ChEMBL CHEMBL3660734 ChEMBL CHEMBL113617 ChEMBL CHEMBL112070 ChEMBL CHEMBL112437 ChEMBL CHEMBL3667546 ChEMBL CHEMBL4061563 ChEMBL CHEMBL120563 ChEMBL CHEMBL326236 ChEMBL CHEMBL3660713 ChEMBL CHEMBL4064364 ChEMBL CHEMBL378577 ChEMBL CHEMBL1562069 ChEMBL CHEMBL449188 ChEMBL CHEMBL3667545 ChEMBL CHEMBL3918259 ChEMBL CHEMBL134275 ChEMBL CHEMBL3128206 ChEMBL CHEMBL491174 ChEMBL CHEMBL4079452 ChEMBL CHEMBL3667542 ChEMBL CHEMBL3660718 ChEMBL CHEMBL111989 ChEMBL CHEMBL494494 ChEMBL CHEMBL4871242 ChEMBL CHEMBL4869675 ChEMBL CHEMBL3667544 ChEMBL CHEMBL4755996 ChEMBL CHEMBL324628 ChEMBL CHEMBL433

Sequence

Primary amino-acid sequence viewer.

MSVFHSNLFRQQALIAGSWRDAADGTTLAVSNPSTGATLGQIPNMGRAEAQQAVDAAAAALPGWRAFTAAQRAALLKNWHRLILENKTALAQIMTAEQGKPLAEAEGEIAYAASFIEWFAEQGKRANGEIIPSPGADKRLMVIRQGVGVCAAITPWNFPAAMITRKAGPALAAGCTMVIKPANETPFTALAMAELANQAGIPQGVINVVTGQSREIGAVFTGDERVRKLSFTGSTEVGRVLMRQCAESIKKLSLELGGNAPFIVFDDADIDKAVEGALIAKFRNAGQTCVCVNRFYIHRAVYDQFCDKFVARVAALKVGDGSESDVQIGPLINADAGRKVQSLLDDALSRGATLLTGGKAHPLGGNFFTPTVIGDVQPGSLLLQEEIFGPVAALVKFDDEQQVIEQANNTIYGLASYFYSNDAARIWRVSEQLEYGMVGINTGLISNEVAPFGGVKQSGLGREGSEHGIEDYLEMKYLCQGL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0009013 Catalysis of the reaction: succinate semialdehyde + NAD(P)+ + H2O = succinate + NAD(P)H + H+.
  • GO:0009450 The chemical reactions and pathways resulting in the breakdown of gamma-aminobutyric acid (GABA).
  • 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: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.

19 records
Show feature table
Start End DB Term Name
258 447 FunFam G3DSA:3.40.309.10:FF:000004 Succinate-semialdehyde dehydrogenase I
30 476 NCBIfam TIGR01780 succinate-semialdehyde dehydrogenase
30 476 InterPro IPR010102 Succinate semialdehyde dehydrogenase
25 472 Gene3D G3DSA:3.40.605.10 Aldehyde Dehydrogenase; Chain A, domain 1
25 472 InterPro IPR016162 Aldehyde dehydrogenase, N-terminal
258 447 Gene3D G3DSA:3.40.309.10 Aldehyde Dehydrogenase; Chain A, domain 2
258 447 InterPro IPR016163 Aldehyde dehydrogenase, C-terminal
30 480 CDD cd07103 ALDH_F5_SSADH_GabD
25 276 FunFam G3DSA:3.40.605.10:FF:000005 Succinate-semialdehyde dehydrogenase I
450 476 FunFam G3DSA:3.40.605.10:FF:000026 Aldehyde dehydrogenase, putative
254 261 ProSitePatterns PS00687 Aldehyde dehydrogenases glutamic acid active site.
254 261 InterPro IPR029510 Aldehyde dehydrogenase, glutamic acid active site
19 477 Pfam PF00171 Aldehyde dehydrogenase family
19 477 InterPro IPR015590 Aldehyde dehydrogenase domain
282 293 ProSitePatterns PS00070 Aldehyde dehydrogenases cysteine active site.
282 293 InterPro IPR016160 Aldehyde dehydrogenase, cysteine active site
5 480 PANTHER PTHR43353 SUCCINATE-SEMIALDEHYDE DEHYDROGENASE, MITOCHONDRIAL
5 481 SUPERFAMILY SSF53720 ALDH-like
5 481 InterPro IPR016161 Aldehyde/histidinol dehydrogenase

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
0.933
Likely same site as P2Rank 2 1.1 Å 15 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
0.852
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.632
Likely same site as FPocket 1 1.1 Å 15 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.079
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.003
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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_A0A0H3GMI2
AlphaFold DB full sequence Viewing
ColabFold KP13_03893
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.

165 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 115 records from similar proteins
Structural ligands 15 0 loaded crystals
Measured bioactivity 100 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
2AK PDB via homolog Detail RCSB PDB
2NO PDB via homolog Detail RCSB PDB
3AK PDB via homolog Detail RCSB PDB
6ZE 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
2AK RCSB PDB P05091 240.1 Da LogP 1.89 TPSA 46.2 ✓ Ro5 ✓ Clean Cc1cc2c(c(c1)Br)NC(=O)C2=O
2NO RCSB PDB P05091 46.0 Da LogP 0.10 TPSA 49.3 ✓ Ro5 ✓ Clean N(=O)[O]
3AK RCSB PDB P05091 237.3 Da LogP 2.42 TPSA 37.4 ✓ Ro5 ✓ Clean c1ccc(cc1)CN2c3ccccc3C(=O)C2=O
6ZE RCSB PDB P05091 270.3 Da LogP 4.42 TPSA 43.4 ✓ Ro5 ✓ Clean CCCC1=C(c2cc3c(c(oc3cc2OC1=O)C)C)C
AE3 RCSB PDB P17202 134.2 Da LogP 0.03 TPSA 38.7 ✓ Ro5 ✓ Clean CCOCCOCCO
B3P RCSB PDB A0A0H2X0S3 282.3 Da LogP -4.01 TPSA 145.4 1 viol. ✓ Clean C(CNC(CO)(CO)CO)CNC(CO)(CO)CO
BTB RCSB PDB P05091 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
BXB RCSB PDB P05091 324.2 Da LogP 3.65 TPSA 47.6 ✓ Ro5 ✓ Clean c1cc(c(c(c1)Cl)C(=O)NCc2ccc3c(c2)OCO3)Cl
CHT RCSB PDB P17202 104.2 Da LogP -0.32 TPSA 20.2 ✓ Ro5 ✓ Clean C[N+](C)(C)CCO
CRD RCSB PDB P05091 70.1 Da LogP 0.76 TPSA 17.1 ✓ Ro5 ✓ Clean C\C=C\C=O
ETX RCSB PDB P17202 90.1 Da LogP 0.02 TPSA 29.5 ✓ Ro5 ✓ Clean CCOCCO
I3E RCSB PDB P05091 162.2 Da LogP 2.84 TPSA 17.1 ✓ Ro5 ✓ Clean CCc1ccc(cc1)C(=O)CC
SIN RCSB PDB P51649 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
TNG RCSB PDB P05091 227.1 Da LogP -1.02 TPSA 157.1 ✓ Ro5 ✓ Clean C(C(CO[N+](=O)[O-])O[N+](=O)[O-])O[N+](=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.