Protein profile

VK055_4639

cysteine desulfurase IscS

Genome: KpATCC43816

Gene: iscS AIK83173.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GWQ1
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Amino acids 404
Annotations 8
Features 20
PDB binders 11
Druggability 0.469

Overview

Basic information about this protein and its source genome.

Accession
VK055_4639
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
iscS AIK83173.1
Status
annotated
Amino acids
404
Structure source
AlphaFold + ColabFold
EC
2.8.1.7
GO
GO:0031071 Catalysis of the reaction: L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine. 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:0044571 The incorporation of two iron atoms and two sulfur atoms into an iron-sulfur cluster. 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: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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
70.667
Human E-value
1.3e-29
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
96.287
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.64

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 0.469
Structure A0A0H3GWQ1
Pocket Pocket 13
P2Rank 0.892
Structure A0A0H3GWQ1
Pocket Pocket 1
ColabFold model
FPocket 0.395 · Pocket 20
P2Rank 0.859 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 262 / 4744 genomes with a hit
Normalized 0.055

Sequence

Primary amino-acid sequence viewer.

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:0031071 Catalysis of the reaction: L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine.
  • 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:0044571 The incorporation of two iron atoms and two sulfur atoms into an iron-sulfur cluster.
  • 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: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 Features

Domain/signature hits 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
2 384 PIRSF PIRSF005572 NifS
2 384 InterPro IPR016454 Cysteine desulfurase
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
1 404 NCBIfam TIGR02006 IscS subfamily cysteine desulfurase
1 404 InterPro IPR010240 Cysteine desulfurase IscS
16 263 FunFam G3DSA:3.40.640.10:FF:000003 Cysteine desulfurase IscS
5 368 Pfam PF00266 Aminotransferase class-V
5 368 InterPro IPR000192 Aminotransferase class V domain
3 384 PANTHER PTHR11601 CYSTEINE DESULFURYLASE FAMILY MEMBER
197 216 ProSitePatterns PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.
197 216 InterPro IPR020578 Aminotransferase class-V, pyridoxal-phosphate binding site
1 395 Hamap MF_00331 Cysteine desulfurase IscS [iscS].
1 395 InterPro IPR010240 Cysteine desulfurase IscS
16 263 Gene3D G3DSA:3.40.640.10 -
16 263 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major 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_A0A0H3GWQ1
AlphaFold — — full sequence — Viewing
ColabFold VK055_4639
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
13 0.469

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 18.25 0.818

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

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
7CET
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
5USR
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
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
DTT
6UXE
Q9Y697 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
EDT
6UXE
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
6WI2
Q9Y697 208.3 Da LogP -0.33 TPSA 57.2 ✓ Ro5 ✓ Clean COCCOCCOCCOCCO
FES
4EB5
O29689 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
HCS
5WT5
O25008 135.2 Da LogP -0.28 TPSA 63.3 ✓ Ro5 ✓ Clean C(CS)[C@@H](C(=O)O)N
P15
6UXE
Q9Y697 296.4 Da LogP -0.29 TPSA 75.6 ✓ Ro5 ✓ Clean COCCOCCOCCOCCOCCOCCO
PDA
5WT6
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
4HVK
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.