Protein target profile

KP13_03545

Cysteine synthase B

Genome: KpKP13 Gene: AHE43351.1 cysM 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GRE2
Length 303
Pocket druggability 0.904
Direct ligand evidence 0 73 total records
Functional annotation 1 EC 2 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 (%)
48.958 Lower values reduce human off-target concern.
Human E-value
1.31e-23
Gut microbiome similarity
3.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
64.189 Higher values support similarity to known essential genes.
DEG E-value
7.619999999999999e-134 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
94.55 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 0.904
Structure A0A0H3GRE2
Pocket Pocket 2
P2Rank 0.877
Structure A0A0H3GRE2
Pocket Pocket 1
ColabFold model
FPocket 0.44 · Pocket 8
P2Rank 0.933 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 157 / 4744 genomes with a hit
Prevalence 3.3%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MNTLEQTIGNTPLVKLQRLGPDNGSEVWVKLEGNNPAGSVKDRAALSMIVEAEKRGEIQPGDVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVSKEQGMEGARDLALEMAQRGEGKLLDQFNNPDNPYAHYTTTGPEIWQQTAGRITHFVSSMGTTGTITGVSRFLREQSKPVTIVGLQPEEGSSIPGIRRWPAEYMPGIFNASLVDTVLDIHQQDAENIMRQLAVREGIFCGVSSGGAVAGALRIARENPGAVVVAIVCDRGDRYLSTGVFGEEHFSQGAGI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 2 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

2
  • GO:0006535 OBSOLETE. The chemical reactions and pathways resulting in the formation of cysteine from L- serine.
  • GO:0004124 Catalysis of the reaction: O3-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
3 289 SUPERFAMILY SSF53686 Tryptophan synthase beta subunit-like PLP-dependent enzymes
3 289 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily
5 292 NCBIfam TIGR01136 cysteine synthase
5 292 InterPro IPR005856 Cysteine synthase
38 147 FunFam G3DSA:3.40.50.1100:FF:000003 Cystathionine beta-synthase
5 281 Pfam PF00291 Pyridoxal-phosphate dependent enzyme
5 281 InterPro IPR001926 Tryptophan synthase beta chain-like, PALP domain
9 288 CDD cd01561 CBS_like
148 289 FunFam G3DSA:3.40.50.1100:FF:000029 Cysteine synthase
30 48 ProSitePatterns PS00901 Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site.
30 48 InterPro IPR001216 Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site
7 289 Gene3D G3DSA:3.40.50.1100 -
7 289 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily
5 293 PANTHER PTHR10314 CYSTATHIONINE BETA-SYNTHASE
3 292 NCBIfam TIGR01138 cysteine synthase B
3 292 InterPro IPR005858 Cysteine synthase CysM
35 140 Gene3D G3DSA:3.40.50.1100 -
35 140 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily

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 #2
0.904
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.877
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Surrounding area
Site 2 P2Rank #2
0.063
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.05
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Surrounding area
Site 4 P2Rank #4
0.006
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Surrounding area
Residue sets
UniProt: Binding site:174-178
UniProt: Binding site:255-255
UniProt: Binding site:71-71
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_A0A0H3GRE2
AlphaFold DB full sequence Viewing
ColabFold KP13_03545
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.

73 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 23 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 15 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3HL PDB via homolog 104.1 Da · LogP -0.16 · TPSA 57.5 Open detail RCSB PDB
4AT PDB via homolog Detail RCSB PDB
4MV PDB via homolog Detail RCSB PDB
AA5 PDB via homolog Detail RCSB PDB
AWH 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
3HL RCSB PDB Q5SLE6 104.1 Da LogP -0.16 TPSA 57.5 ✓ Ro5 ✓ Clean C[C@@H](CC(=O)O)O
4AT RCSB PDB Q5SLE6 130.1 Da LogP 0.83 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)CCCC(=O)O
4MV RCSB PDB Q5SLE6 116.2 Da LogP 1.51 TPSA 37.3 ✓ Ro5 ✓ Clean CC(C)CCC(=O)O
AA5 RCSB PDB P47998 378.3 Da LogP 1.33 TPSA 149.5 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)C=N[C@@H](CCSC)C(=O)O)O
AWH RCSB PDB P9WP55 412.4 Da LogP 3.08 TPSA 116.5 ✓ Ro5 ✓ Clean CN\1C(=O)/C(=C/c2ccccc2OCC(=O)O)/S/C1=N\c3cccc(…
C6P RCSB PDB I1L6I6 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
PDA RCSB PDB P9WP55 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
PUS RCSB PDB D2Z027 392.3 Da LogP -0.82 TPSA 213.9 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@@H](CONC(=O)N)…

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.