Protein target profile

VK055_0027

D-cysteine desulfhydrase monomer

Genome: KpATCC43816 Gene: dcyD AIK78658.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GVK9

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Length 328

Pocket druggability 0.911

Direct ligand evidence 0 34 total records

Functional annotation 1 EC 3 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.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.93. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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: No hit
Gut microbiome similarity: 2.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 97.04 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 0.911

Structure A0A0H3GVK9

Pocket Pocket 1

P2Rank 0.934

Structure A0A0H3GVK9

Pocket Pocket 1

ColabFold model

FPocket 0.928 · Pocket 2

P2Rank 0.914 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 100 / 4744 genomes with a hit

Prevalence 2.1%

Cross-references

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

Sequence

UniProt A0A0H3GVK9

Sequence

Primary amino-acid sequence viewer.

MSLQNLTRFPRLELIGAPTPLEYLPRLSDHLGREIFIKRDDTTPLAMGGNKLRKLEFLAADALREGADTLITAGAIQSNHVRQTAAVAAKLGLHCVALLENPIGTRAENYLSNGNRLLLDLFNTQVEMCDALTDPAAQLDELATRIEAQGYRPYVIPVGGSNALGALGYVESALEISQQCEDAVAISSVVVASGSAGTHAGLAVGLEQLMPQAELIGVTVSRSVADQLPKVEALQQAVANSLELQAKAEIILWDDYFAPGYGTPNEDGMAAVKLLAQLEGILLDPVYTGKAMAGLIDGITQKRFKDEGPILFVHTGGAPALFAYHPHL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

4.4.1.15

Gene Ontology (GO)

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:0019148 Catalysis of the reaction: D-cysteine + H2O = hydrogen sulfide + pyruvate + NH4+ + H+.
GO:0046416 The chemical reactions and pathways involving D-amino acids, the D-enantiomers of amino acids.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
50	158	FunFam	G3DSA:3.40.50.1100:FF:000017	D-cysteine desulfhydrase
7	326	SUPERFAMILY	SSF53686	Tryptophan synthase beta subunit-like PLP-dependent enzymes
7	326	InterPro	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily
15	316	Pfam	PF00291	Pyridoxal-phosphate dependent enzyme
15	316	InterPro	IPR001926	Tryptophan synthase beta chain-like, PALP domain
50	158	Gene3D	G3DSA:3.40.50.1100	-
50	158	InterPro	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily
12	328	NCBIfam	TIGR01275	pyridoxal phosphate-dependent enzymes, D-cysteine desulfhydrase family
12	328	InterPro	IPR005966	D-cysteine desulfhydrase
1	328	PIRSF	PIRSF006278	ACCD_DCysDesulf
1	328	InterPro	IPR027278	1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase
10	319	Gene3D	G3DSA:3.40.50.1100	-
10	319	InterPro	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily
1	328	Hamap	MF_01045	D-cysteine desulfhydrase [dcyD].
1	328	InterPro	IPR023702	D-cysteine desulphhydrase, bacterial
7	323	PANTHER	PTHR43780	1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE-RELATED
7	323	InterPro	IPR027278	1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase
19	317	CDD	cd06449	ACCD

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 #1

0.911

Likely same site as P2Rank 1 2.2 Å 19 shared residues 83% of smaller site

Unusual size

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Surrounding area

Site 2 FPocket #13

0.268

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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.934

Likely same site as FPocket 1 2.2 Å 19 shared residues 83% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.022

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Surrounding area

Site 3 P2Rank #3

0.012

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Surrounding area

Site 4 P2Rank #4

0.009

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Surrounding area

Site 5 P2Rank #5

0.003

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Surrounding area

Residue sets

UniProt: Active site:78-78 Nucleophile

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #2

0.928

Likely same site as P2Rank 3 6.1 Å 9 shared residues 100% of smaller site

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Surrounding area

Site 2 FPocket #1

0.277

Likely same site as P2Rank 1 1.0 Å 24 shared residues 92% of smaller site

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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.914

Likely same site as FPocket 1 1.0 Å 24 shared residues 92% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.035

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Surrounding area

Site 3 P2Rank #3

0.027

Likely same site as FPocket 2 6.1 Å 9 shared residues 100% of smaller site

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Surrounding area

Site 4 P2Rank #4

0.005

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Surrounding area

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_A0A0H3GVK9	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_0027	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.

34 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 10 records from similar proteins

Structural ligands 10 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 24 similarity-based ZINC candidates

Best available ligand signal

1AC PDB via homolog 101.1 Da · LogP -0.44 · TPSA 63.3 Open detail RCSB PDB

2KT PDB via homolog Detail RCSB PDB

5PA PDB via homolog Detail RCSB PDB

A3B PDB via homolog Detail RCSB PDB

BEN PDB via homolog Detail RCSB PDB

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
1AC RCSB PDB	1TZ2	Q00740	101.1 Da LogP -0.44 TPSA 63.3	✓ Ro5	✓ Clean	`C1CC1(C(=O)O)N`
2KT RCSB PDB	1TZK	Q00740	102.1 Da LogP 0.05 TPSA 54.4	✓ Ro5	✓ Clean	`CCC(=O)C(=O)O`
5PA RCSB PDB	1J0B	O57809	332.2 Da LogP 0.41 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CNC2(CC2)C(=O)O)O`
A3B RCSB PDB	1TZJ	Q00740	101.1 Da LogP -2.47 TPSA 67.8	✓ Ro5	✓ Clean	`C=C[C@H](C(=O)[O-])[NH3+]`
BEN RCSB PDB	4D8T	Q8ZNT7	120.2 Da LogP 0.97 TPSA 49.9	✓ Ro5	✓ Clean	`[H]/N=C(\c1ccccc1)/N`
DCS RCSB PDB	4D9F	Q8ZNT7	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`
LCS RCSB PDB	4D9E	Q8ZNT7	331.2 Da LogP -0.29 TPSA 150.6	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)C/N=C/2\CONC2=O)O`
MLP RCSB PDB	1RQX	Q00740	136.1 Da LogP -1.02 TPSA 86.4	✓ Ro5	✓ Clean	`C1CC1(N)[P@](=O)(O)[O-]`
PMP RCSB PDB	4D9B	Q8ZNT7	248.2 Da LogP 0.16 TPSA 125.9	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CN)O`
PYR RCSB PDB	4D8W	Q8ZNT7	88.1 Da LogP -0.34 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)C(=O)O`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC4964174 ZINC	1.000	202.2 Da LogP -0.88 TPSA 126.6	✓ Ro5	✓ Clean	`NC1(C(=O)O)CCC(N)(C(=O)O)CC1`
ZINC1532705 ZINC	0.769	249.2 Da LogP 0.20 TPSA 120.1	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CO)c1O`
ZINC19433130 ZINC	0.722	227.3 Da LogP 3.07 TPSA 63.3	✓ Ro5	✓ Clean	`NC1(C(=O)O)CCCCCCCCCCC1`
ZINC1656021 ZINC	0.692	233.2 Da LogP 1.01 TPSA 99.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C)c1O`
ZINC1532514 ZINC	0.643	247.1 Da LogP 0.52 TPSA 117.0	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C=O)c1O`
ZINC2511705 ZINC	0.636	201.2 Da LogP 0.09 TPSA 81.8	✓ Ro5	✓ Clean	`NC1(C(=O)O)CCC2(CC1)OCCO2`
ZINC68576964 ZINC	0.636	226.2 Da LogP 0.60 TPSA 89.3	✓ Ro5	✓ Clean	`NC1(C(=O)O)CCC(N)(C(F)(F)F)CC1`
ZINC1532708 ZINC	0.620	248.2 Da LogP 0.16 TPSA 125.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CN)c1O`
ZINC68576962 ZINC	0.609	227.2 Da LogP 0.64 TPSA 83.6	✓ Ro5	✓ Clean	`NC1(C(=O)O)CCC(O)(C(F)(F)F)CC1`
ZINC100053590 ZINC	0.524	217.2 Da LogP -1.04 TPSA 137.9	✓ Ro5	✓ Clean	`N[C@]1(C(=O)O)C[C@H](C(=O)O)[C@H](C(=O)O)C1`
ZINC100763462 ZINC	0.524	217.2 Da LogP -1.04 TPSA 137.9	✓ Ro5	✓ Clean	`N[C@@]1(C(=O)O)C[C@H](C(=O)O)[C@H](C(=O)O)C1`
ZINC1529994 ZINC	0.523	219.1 Da LogP -0.02 TPSA 118.6	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(N)n1`
ZINC82862625 ZINC	0.520	211.2 Da LogP 1.52 TPSA 63.3	✓ Ro5	✓ Clean	`NC1(C(=O)O)CCC(C(F)(F)F)CC1`
ZINC953109649 ZINC	0.520	211.2 Da LogP 1.52 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@]1(C(=O)O)CC[C@H](C(F)(F)F)CC1`
ZINC2114966 ZINC	0.519	332.2 Da LogP 0.99 TPSA 149.5	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(/C=N/CCCC(=O)O)c1O`
ZINC13213450 ZINC	0.509	350.3 Da LogP 0.49 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c([C@@H]2N[C@H](C(=O)O)CS2)c…`
ZINC13213453 ZINC	0.509	350.3 Da LogP 0.49 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c([C@H]2N[C@H](C(=O)O)CS2)c1O`
ZINC13213455 ZINC	0.509	350.3 Da LogP 0.49 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c([C@@H]2N[C@@H](C(=O)O)CS2)…`
ZINC13213457 ZINC	0.509	350.3 Da LogP 0.49 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c([C@H]2N[C@@H](C(=O)O)CS2)c…`
ZINC100368719 ZINC	0.500	210.3 Da LogP 2.43 TPSA 52.0	✓ Ro5	✓ Clean	`N/C(=C(\N)c1ccccc1)c1ccccc1`
ZINC24716871 ZINC	0.500	210.3 Da LogP 2.43 TPSA 52.0	✓ Ro5	✓ Clean	`N/C(=C(/N)c1ccccc1)c1ccccc1`
ZINC5771971 ZINC	0.500	238.3 Da LogP 1.71 TPSA 76.8	✓ Ro5	✓ Clean	`N/C(=N\N=C(/N)c1ccccc1)c1ccccc1`
ZINC584905825 ZINC	0.500	201.3 Da LogP 1.66 TPSA 63.3	✓ Ro5	✓ Clean	`C[Si]1(C)CCC[C@](N)(C(=O)O)CC1`
ZINC584905826 ZINC	0.500	201.3 Da LogP 1.66 TPSA 63.3	✓ Ro5	✓ Clean	`C[Si]1(C)CCC[C@@](N)(C(=O)O)CC1`

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.