Protein target profile

VK055_4350

cysteine desulfurase, catalytic subunit CsdA

Genome: KpATCC43816 Gene: csdA AIK82893.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 19 reactions UniProt A0A0H3GSG6
Length 401
Pocket druggability 0.279
Metabolic reactions 19
Chokepoint Yes
Direct ligand evidence 0 54 total records
Functional annotation 1 EC 5 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 (%)
30.114 Lower values reduce human off-target concern.
Human E-value
2.07e-07
Gut microbiome similarity
2.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
82.294 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
95.44 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 0.279
Structure A0A0H3GSG6
Pocket Pocket 1
P2Rank 0.756
Structure A0A0H3GSG6
Pocket Pocket 1
ColabFold model
FPocket 0.178 · Pocket 13
P2Rank 0.743 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 107 / 4744 genomes with a hit
Prevalence 2.3%

Cross-references

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

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a consuming chokepoint reaction in Thiamine metabolism, more central than 98.8% of genes in this genome.

Relative network centrality 98.8% more central than 98.8% of genes in this genome
Chokepoint Chokepoint gene
Catalyzed reactions

19 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MNAFNPAHFRAQFPALADAGVYLDSAATALKPLAVIDASDQFYRLSAGNVHRSQFAAAQRLTERYEAARDRVAAWLNAPSGKDIVWTRGTTEAINMVAQSYVRPRLQPGDEIIVSEAEHHANLVPWLMVAGQTGARVVKLPLGADRLPDIASLSALITPRSRVLAIGQMSNVTGGCPDLAQAIRLAHAAGMVVMVDGAQGAVHFPADVQALDIDFYAFSGHKLYGPTGIGALYGKSELLAAMSPWLGGGKMIAEVSFDGFTPQPAPYGLEAGTPNVAGVIGLSAALEWLAQSDIGQAENWSRSLASLAEEELAKRPGFRSFRCQQSSLLAFEFEGIHHSDLVTLLAESGIALRAGQHCAQPLLAALGVSGTLRASFAPYNTQDDVAALVHAVDRALEILVD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0016226 The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0006534 OBSOLETE. The chemical reactions and pathways involving cysteine, 2-amino-3-mercaptopropanoic acid.
  • GO:0031071 Catalysis of the reaction: L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine.
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
7 396 PANTHER PTHR43586 CYSTEINE DESULFURASE
5 397 SUPERFAMILY SSF53383 PLP-dependent transferases
5 397 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
21 392 CDD cd06453 SufS_like
21 392 InterPro IPR010970 Cysteine desulfurase, SufS
34 292 Gene3D G3DSA:3.40.640.10 -
34 292 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
21 389 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
21 389 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
4 401 NCBIfam TIGR03392 cysteine desulfurase CsdA
4 401 InterPro IPR022471 Cysteine desulphurase, catalytic subunit, CsdA
34 292 FunFam G3DSA:3.40.640.10:FF:000081 Cysteine desulfurase CsdA
58 78 Coils Coil Coil
213 232 ProSitePatterns PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.
213 232 InterPro IPR020578 Aminotransferase class-V, pyridoxal-phosphate binding site
21 388 Pfam PF00266 Aminotransferase class-V
21 388 InterPro IPR000192 Aminotransferase class V domain

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
0.279
Likely same site as P2Rank 1 2.4 Å 20 shared residues 80% 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
0.756
Likely same site as FPocket 1 2.4 Å 20 shared residues 80% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.164
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Surrounding area
Site 3 P2Rank #3
0.14
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Surrounding area
Site 4 P2Rank #4
0.091
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Surrounding area
Site 5 P2Rank #5
0.026
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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_A0A0H3GSG6
AlphaFold DB full sequence Viewing
ColabFold VK055_4350
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.

54 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 45 similarity-based ZINC candidates
Best available ligand signal
7TS PDB via homolog 331.2 Da · LogP 0.60 · TPSA 157.9 Open detail RCSB PDB
C6P PDB via homolog Detail RCSB PDB
CKT PDB via homolog Detail RCSB PDB
DCS PDB via homolog Detail RCSB PDB
LPG 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
7TS RCSB PDB O32164 331.2 Da LogP 0.60 TPSA 157.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=CONC2=O)O
C6P RCSB PDB A0A1I5NEH3 352.3 Da LogP 0.18 TPSA 149.2 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CS)C(=O)O)O
CKT RCSB PDB P77444 350.3 Da LogP 0.66 TPSA 149.5 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)C/N=C(\CS)/C(=O)O)O
DCS RCSB PDB O32164 333.2 Da LogP -0.78 TPSA 150.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2CONC2=O)O
LPG RCSB PDB P77444 99.1 Da LogP -0.97 TPSA 63.3 ✓ Ro5 ✓ Clean C#CC(C(=O)O)N
PDA RCSB PDB O32164 320.2 Da LogP 0.27 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNC(C)C(=O)O)O
PMP RCSB PDB O32164 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
SEC RCSB PDB P77444 168.1 Da LogP -1.28 TPSA 63.3 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)N)[SeH]
TLA RCSB PDB Q46925 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=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.