Protein profile

VK055_0027

D-cysteine desulfhydrase monomer

Genome: KpATCC43816

Gene: AIK78658.1 dcyD Structure source: AlphaFold + ColabFold UniProt A0A0H3GVK9

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Amino acids 328

Annotations 4

Features 18

PDB binders 10

Druggability 0.911

Overview

Basic information about this protein and its source genome.

Accession: VK055_0027
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK78658.1 dcyD
Status: annotated
Amino acids: 328
Structure source: AlphaFold + ColabFold

4.4.1.15

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.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 97.04

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 0.911

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

Normalized 0.021

Sequence

Primary amino-acid sequence viewer.

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 Features

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

Loading 3D structure...

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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_A0A0H3GVK9	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_0027	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				0.911
13				0.268

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				22.48	0.881
2				1.18	0.01

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
2				0.928
1				0.277

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				18.83	0.831

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

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, 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	1TZ2	Q00740	101.1 Da LogP -0.44 TPSA 63.3	✓ Ro5	✓ Clean	`C1CC1(C(=O)O)N`
2KT	1TZK	Q00740	102.1 Da LogP 0.05 TPSA 54.4	✓ Ro5	✓ Clean	`CCC(=O)C(=O)O`
5PA	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	1TZJ	Q00740	101.1 Da LogP -2.47 TPSA 67.8	✓ Ro5	✓ Clean	`C=C[C@H](C(=O)[O-])[NH3+]`
BEN	4D8T	Q8ZNT7	120.2 Da LogP 0.97 TPSA 49.9	✓ Ro5	✓ Clean	`[H]/N=C(\c1ccccc1)/N`
DCS	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	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	1RQX	Q00740	136.1 Da LogP -1.02 TPSA 86.4	✓ Ro5	✓ Clean	`C1CC1(N)[P@](=O)(O)[O-]`
PMP	4D9B	Q8ZNT7	248.2 Da LogP 0.16 TPSA 125.9	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CN)O`
PYR	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	1.000	202.2 Da LogP -0.88 TPSA 126.6	✓ Ro5	✓ Clean	`NC1(C(=O)O)CCC(N)(C(=O)O)CC1`
ZINC1532705	0.769	249.2 Da LogP 0.20 TPSA 120.1	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CO)c1O`
ZINC19433130	0.722	227.3 Da LogP 3.07 TPSA 63.3	✓ Ro5	✓ Clean	`NC1(C(=O)O)CCCCCCCCCCC1`
ZINC1656021	0.692	233.2 Da LogP 1.01 TPSA 99.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C)c1O`
ZINC1532514	0.643	247.1 Da LogP 0.52 TPSA 117.0	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C=O)c1O`
ZINC2511705	0.636	201.2 Da LogP 0.09 TPSA 81.8	✓ Ro5	✓ Clean	`NC1(C(=O)O)CCC2(CC1)OCCO2`
ZINC68576964	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	0.620	248.2 Da LogP 0.16 TPSA 125.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CN)c1O`
ZINC68576962	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	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	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	0.523	219.1 Da LogP -0.02 TPSA 118.6	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(N)n1`
ZINC82862625	0.520	211.2 Da LogP 1.52 TPSA 63.3	✓ Ro5	✓ Clean	`NC1(C(=O)O)CCC(C(F)(F)F)CC1`
ZINC953109649	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	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	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	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	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	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	0.500	210.3 Da LogP 2.43 TPSA 52.0	✓ Ro5	✓ Clean	`N/C(=C(\N)c1ccccc1)c1ccccc1`
ZINC24716871	0.500	210.3 Da LogP 2.43 TPSA 52.0	✓ Ro5	✓ Clean	`N/C(=C(/N)c1ccccc1)c1ccccc1`
ZINC5771971	0.500	238.3 Da LogP 1.71 TPSA 76.8	✓ Ro5	✓ Clean	`N/C(=N\N=C(/N)c1ccccc1)c1ccccc1`
ZINC584905825	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	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.