Protein profile

VK055_4350

cysteine desulfurase, catalytic subunit CsdA

Genome: KpATCC43816

Gene: AIK82893.1 csdA Structure source: AlphaFold + ColabFold UniProt A0A0H3GSG6
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Amino acids 401
Annotations 6
Features 17
PDB binders 9
Druggability 0.279

Overview

Basic information about this protein and its source genome.

Accession
VK055_4350
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82893.1 csdA
Status
annotated
Amino acids
401
Structure source
AlphaFold + ColabFold
EC
2.8.1.7
GO
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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
30.114
Human E-value
2.07e-07
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
82.294
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.44

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its 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
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GSG6
AlphaFold — — full sequence — Viewing
ColabFold VK055_4350
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
1 0.279

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 12.03 0.636
2 3.63 0.136
3 2.75 0.083
4 2.28 0.057

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

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
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
5ZSS
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
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
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
1I29
P77444 99.1 Da LogP -0.97 TPSA 63.3 ✓ Ro5 ✓ Clean C#CC(C(=O)O)N
PDA
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
7CEO
O32164 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
SEC
1KMK
P77444 168.1 Da LogP -1.28 TPSA 63.3 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)N)[SeH]
TLA
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.