Protein target profile

KP13_00845

Cysteine desulfurase

Genome: KpKP13 Gene: iscS AHE43209.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GWQ1
Length 404
Pocket druggability 0.469
Direct ligand evidence 0 61 total records
Functional annotation 1 EC 7 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 (%)
70.667 Lower values reduce human off-target concern.
Human E-value
1.3e-29
Gut microbiome similarity
5.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
96.287 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
95.66 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 0.469
Structure A0A0H3GWQ1
Pocket Pocket 13
P2Rank 0.892
Structure A0A0H3GWQ1
Pocket Pocket 1
ColabFold model
FPocket 0.473 · Pocket 23
P2Rank 0.86 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 262 / 4744 genomes with a hit
Prevalence 5.5%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MKLPIYLDYSATTPVDPRVAEKMMQFLTMDGTFGNPASRSHRFGWQAEEAVDIARNQIAELVGADPREIVFTSGATESDNLAIKGAANFYQKKGKHIITSKTEHKAVLDTCRQLEREGFEVTYLAPQSNGIIDLKELEAAMRDDTILVSIMHVNNEIGVVQDIATIGEMCRARGIIYHVDATQSVGKLPIDLSQLKVDLMSFSGHKIYGPKGIGALYVRRKPRIRIEAQIHGGGHERGMRSGTLPVHQIVGMGEAYRIAKEEMESEMARLRTLRNRLWNGVKDMEEVYLNGDLEQGAPNILNVSFNYVEGESLIMALKDLAVSSGSACTSASLEPSYVLRALGMTDELAHSSIRFSLGRFTTEEEIDYAIDLIRKSIGRLRELSPLWEMFKQGVDLNSIEWSHH

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • GO:0031071 Catalysis of the reaction: L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine.
  • GO:0044571 The incorporation of two iron atoms and two sulfur atoms into an iron-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:1990221 A protein complex capable of cysteine desulfurase activity decomposing L-cysteine to L-alanine and sulfur. It belongs to a ubiquitous family of pyridoxal 5-phosphate (PLP)-dependent enzymes.
  • GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
257 368 FunFam G3DSA:3.90.1150.10:FF:000002 Cysteine desulfurase IscS
5 390 SUPERFAMILY SSF53383 PLP-dependent transferases
5 390 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
5 368 Pfam PF00266 Aminotransferase class-V
5 368 InterPro IPR000192 Aminotransferase class V domain
5 368 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
5 368 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
256 276 Coils Coil Coil
2 384 PIRSF PIRSF005572 NifS
2 384 InterPro IPR016454 Cysteine desulfurase
197 216 ProSitePatterns PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.
197 216 InterPro IPR020578 Aminotransferase class-V, pyridoxal-phosphate binding site
16 263 FunFam G3DSA:3.40.640.10:FF:000003 Cysteine desulfurase IscS
1 404 NCBIfam TIGR02006 IscS subfamily cysteine desulfurase
1 404 InterPro IPR010240 Cysteine desulfurase IscS
16 263 Gene3D G3DSA:3.40.640.10 -
16 263 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
1 395 Hamap MF_00331 Cysteine desulfurase IscS [iscS].
1 395 InterPro IPR010240 Cysteine desulfurase IscS
3 384 PANTHER PTHR11601 CYSTEINE DESULFURYLASE FAMILY MEMBER

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 #13
0.469
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.892
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.02
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.02
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.001
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:328-328 Cysteine persulfide intermediate
UniProt: Binding site:155-155
UniProt: Binding site:183-183
UniProt: Binding site:203-205
UniProt: Binding site:243-243
UniProt: Binding site:328-328 via persulfide group
UniProt: Binding site:75-76
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_A0A0H3GWQ1
AlphaFold DB full sequence Viewing
ColabFold KP13_00845
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.

61 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 11 records from similar proteins
Structural ligands 11 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 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
8Q1 PDB via homolog Detail RCSB PDB
C6P PDB via homolog Detail RCSB PDB
DTT PDB via homolog Detail RCSB PDB
EDT 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 O25008 331.2 Da LogP 0.60 TPSA 157.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=CONC2=O)O
8Q1 RCSB PDB Q9Y697 540.7 Da LogP 3.29 TPSA 162.3 1 viol. ✓ Clean CCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)…
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
DTT RCSB PDB Q9Y697 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
EDT RCSB PDB Q9Y697 292.2 Da LogP -2.07 TPSA 155.7 ✓ Ro5 ✓ Clean C(CN(CC(=O)O)CC(=O)O)N(CC(=O)O)CC(=O)O
ETE RCSB PDB Q9Y697 208.3 Da LogP -0.33 TPSA 57.2 ✓ Ro5 ✓ Clean COCCOCCOCCOCCO
FES RCSB PDB O29689 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
HCS RCSB PDB O25008 135.2 Da LogP -0.28 TPSA 63.3 ✓ Ro5 ✓ Clean C(CS)[C@@H](C(=O)O)N
P15 RCSB PDB Q9Y697 296.4 Da LogP -0.29 TPSA 75.6 ✓ Ro5 ✓ Clean COCCOCCOCCOCCOCCOCCO
PDA RCSB PDB O25008 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 O29689 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)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.