Protein target profile

PA3667

cysteine desulfurase

Genome: NC_002516.2

Gene: PA3667 csd 3D evidence: AlphaFold DB model UniProt Q9HXX3
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Length 401
Pocket druggability 0.696
Ligand records 59
EC / GO 1 / 4
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

3 signals

Strengths

Moderate predicted binding pocket FPocket selected-pocket score 0.70. This supports review but is not experimental validation. Structure available AlphaFold DB model Ligand evidence via structure/bioactivity 9 structural and 0 bioactivity records.

Risks / watch

Human similarity Top human hit identity: 37.349%.

Missing evidence

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.
How to read 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 TPW 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.

Overview

Basic information about this protein and its source genome.

Accession
PA3667
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA3667 csd
Status
annotated
Amino acids
401
3D evidence
AlphaFold DB model
EC
2.8.1.7
GO
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. GO:0006534 OBSOLETE. The chemical reactions and pathways involving cysteine, 2-amino-3-mercaptopropanoic acid. 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.

Target profile

Computed evidence for target prioritization.

Human off-target
Hit
Human identity (%)
37.349
Human E-value
6.32e-06
Gut microbiome off-target
Hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected pocket evidence

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 0.696
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MSLPSPWRADFPAFSAFAAEGLTYLDSAATAQKPQAVLDALNGYYLGGAANVHRAQHVPGERATRAFEAARSRVAHWLHAGNPAEVLFTRGTTEAINLVAYGLERHFRPGDELLVSALEHHANLLPWQQLALRRGLVLRVLPLDERGVIDLEQARHIIGERTRLLAISQLSNVLGTWQPVVELIQLARERGAWTLVDGAQGSVHGRHDLPGLGCDFYAFSGHKLYGPDGIGVLWGRPQALEQLAHWQFGGEMVRHTGFHEASFHAAPLGFEAGTPAVSAAIGLGATIDWLATLDEAEVAAHEGALHARLLAGLLARDGVSLLGEPQAALASFCVDGVHVADLAHLLGEQGIAVRAGHHCAMPLLQRLEVPGALRVSLGLYNDADDLERFFLALDRSLELLR

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • 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.
  • GO:0006534 OBSOLETE. The chemical reactions and pathways involving cysteine, 2-amino-3-mercaptopropanoic acid.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
214 233 ProSitePatterns PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.
214 233 InterPro IPR020578 Aminotransferase class-V, pyridoxal-phosphate binding site
9 390 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
9 390 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
7 396 PANTHER PTHR43586 CYSTEINE DESULFURASE
24 389 Pfam PF00266 Aminotransferase class-V
24 389 InterPro IPR000192 Aminotransferase class V domain
6 398 SUPERFAMILY SSF53383 PLP-dependent transferases
6 398 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
41 298 Gene3D G3DSA:3.40.640.10 -
41 298 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
23 393 CDD cd06453 SufS_like
23 393 InterPro IPR010970 Cysteine desulfurase, SufS

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.

3D visualization script Full viewer

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Structural evidence

0 + 1

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 PA3667
AlphaFold DB — — full sequence — Viewing
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
0.696
Show in viewer
Site 2 FPocket #5
0.377
Show in viewer

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.

59 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 59 via homologs
Structural ligands 9 0 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 44 0 PAINS alerts
Best available ligand signal
7TS PDB via homolog 331.2 Da · LogP 0.60 · TPSA 157.9 Open detail RCSB PDB
Detail RCSB PDB 7TS PDB via homolog
Detail RCSB PDB C6P PDB via homolog
Detail RCSB PDB CKT PDB via homolog
Detail RCSB PDB DCS PDB via homolog

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
7CES
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
5ZSO
O32164 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
6O13
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
7CER
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
1I29
P77444 99.1 Da LogP -0.97 TPSA 63.3 ✓ Ro5 ✓ Clean C#CC(C(=O)O)N
PDA RCSB PDB
5XT6
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
7CEO
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
1KMK
P77444 168.1 Da LogP -1.28 TPSA 63.3 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)N)[SeH]
TLA RCSB PDB
5FT5
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.