Protein profile

VK055_1567

thiol reductant ABC exporter, CydD subunit

Genome: KpATCC43816

Gene: cydD AIK80187.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GKY7
Amino acids 588
Annotations 8
Features 46
PDB binders 4
Druggability 0.682

Overview

Basic information about this protein and its source genome.

Accession
VK055_1567
Gene
cydD AIK80187.1
Status
annotated
Amino acids
588
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
42.424
Human E-value
3.8e-10
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
81.293
DEG E-value
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
91.32

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 0.682
Structure A0A0H3GKY7
Pocket Pocket 16
P2Rank 0.612
Structure A0A0H3GKY7
Pocket Pocket 1
ColabFold model
FPocket 0.721 · Pocket 45
P2Rank 0.192 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 126 / 4744 genomes with a hit
Normalized 0.027

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

8
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0042883 The directed movement of cysteine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0140359 Primary active transporter characterized by two nucleotide-binding domains and two transmembrane domains. Uses the energy generated from ATP hydrolysis to drive the transport of a substance across a membrane.
  • GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0034040 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + lipid(in) = ADP + phosphate + lipid(out).

Sequence Features

Domain/signature hits from InterPro and related databases.

46 records
Show feature table
Start End DB Term Name
486 500 ProSitePatterns PS00211 ABC transporters family signature.
486 500 InterPro IPR017871 ABC transporter-like, conserved site
25 292 Pfam PF00664 ABC transporter transmembrane region
25 292 InterPro IPR011527 ABC transporter type 1, transmembrane domain
29 316 ProSiteProfiles PS50929 ABC transporter integral membrane type-1 fused domain profile.
29 316 InterPro IPR011527 ABC transporter type 1, transmembrane domain
245 267 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
273 277 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
342 588 FunFam G3DSA:3.40.50.300:FF:000980 Cysteine/glutathione ABC transporter permease/ATP-binding protein CydD
21 556 NCBIfam TIGR02857 thiol reductant ABC exporter subunit CydD
21 556 InterPro IPR014216 ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD
345 588 Gene3D G3DSA:3.40.50.300 -
345 588 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
51 580 PANTHER PTHR24221 ATP-BINDING CASSETTE SUB-FAMILY B
51 580 InterPro IPR039421 Type 1 protein exporter
167 188 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
351 582 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
351 582 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
140 161 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
350 583 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile.
350 583 InterPro IPR003439 ABC transporter-like, ATP-binding domain
29 324 CDD cd18584 ABC_6TM_AarD_CydD
162 166 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
375 560 SMART SM00382 AAA_5
375 560 InterPro IPR003593 AAA+ ATPase domain
282 304 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
189 244 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
23 45 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
80 139 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
2 332 FunFam G3DSA:1.20.1560.10:FF:000039 Cysteine/glutathione ABC transporter permease/ATP-binding protein CydD
245 272 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
11 331 SUPERFAMILY SSF90123 ABC transporter transmembrane region
11 331 InterPro IPR036640 ABC transporter type 1, transmembrane domain superfamily
60 82 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
137 159 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
369 513 Pfam PF00005 ABC transporter
369 513 InterPro IPR003439 ABC transporter-like, ATP-binding domain
21 45 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
3 331 Gene3D G3DSA:1.20.1560.10 ABC transporter type 1, transmembrane domain
3 331 InterPro IPR036640 ABC transporter type 1, transmembrane domain superfamily
57 79 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
298 588 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
278 297 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
46 56 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
163 185 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.

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_A0A0H3GKY7
AlphaFold full sequence Viewing
ColabFold VK055_1567
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
16 0.682
31 0.008
5 0.003
36 0.001

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 13.7 0.612
2 5.89 0.238
3 5.51 0.218
4 4.22 0.142
5 2.83 0.071

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
0SA P34712 512.7 Da LogP -0.13 TPSA 169.3 3 viol. ✓ Clean CCCCCCCCCCCS[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)…
AGS Q9WYC4 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP P63359 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
O34 Q1RAG2 481.7 Da LogP 2.66 TPSA 114.5 ✓ Ro5 ✓ Clean C[C@@]1(CSC(=N1)C(C)(C)[C@@H]([C@@H]2CS[C@@H](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.