Protein target profile

KP13_04219

ATP-binding/permease protein cydC

Genome: KpKP13 Gene: AHE45450.1 cydC 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GUY5
Length 573
Pocket druggability 0.904
Direct ligand evidence 0 54 total records
Functional annotation 0 EC 11 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 (%)
51.111 Lower values reduce human off-target concern.
Human E-value
5.13e-07
Gut microbiome similarity
2.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
81.501 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
92.48 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 A0A0H3GUY5
Pocket Pocket 35
P2Rank 0.324
Structure A0A0H3GUY5
Pocket Pocket 1
ColabFold model
FPocket 0.645 · Pocket 48
P2Rank 0.288 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 122 / 4744 genomes with a hit
Prevalence 2.6%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MRALLPYLALYKRHKWMLLLGVVLAIVTLLASIGLLTLSGWFLSASAVVGVAGIYSFNYMLPAAGVRGAAIIRTAGRYFERLVSHDATFRVLQHLRVFTFSKLLPLSPAGLARFRQGELLNRVVADVDTLDHLYLRVISPLVGALVVIVVVTCGLSLLDVTLALTLGGIMLATLLVMPPLFYRAGKPAGESMTQLRGQYRQQLTAWLQGQAELMVFNASDRYRAQMEKTELSWQDAQRRQAELTALSQAVMLLIGGIAVVAMLWLASDGVGGNSQPGALIALFVFCALAAFEALAPVTGAFQHLGQVIASARRISQITDQQPEVTFVEDEASPPAQVALTLQEVTFRYPQQPSPALENISLQIAAGEHIAILGRTGCGKSTLLQLLTRAWDPSQGEILLNNQPLSGLSEATLRQAMSVVPQRVHLFSATLRDNLLLAAPEADDAHLSATLEKVGLEKLLQDGGLNGWLGEGGRQLSGGELRRLAIARALLHDAPLMLLDEPTEGLDAATESQILHLLADVMRDKTVLMVTHRLRGLAGFNQIIVMDNGQIIEQGSHAELLAKQGRYFQFKQRL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

11 GO

Gene Ontology (GO)

11
  • 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:0042626 Primary active transporter of a solute across a membrane, via the reaction: ATP + H2O = ADP + phosphate, to directly drive the transport of a substance across a membrane. The transport protein may be transiently phosphorylated (P-type transporters), or not (ABC-type transporters and other families of transporters). Primary active transport occurs up the solute's concentration gradient and is driven by a primary energy source.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0034775 A process in which glutathione is transported across a membrane.
  • GO:0045454 Any process that maintains the redox environment of a cell or compartment within a cell.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • 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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0015421 Catalysis of the reaction: ATP + H2O + oligopeptide(out) = ADP + phosphate + oligopeptide(in).
  • GO:0006865 The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

47 records
Show feature table
Start End DB Term Name
25 314 CDD cd18585 ABC_6TM_CydC
137 157 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 322 Gene3D G3DSA:1.20.1560.10 ABC transporter type 1, transmembrane domain
1 322 InterPro IPR036640 ABC transporter type 1, transmembrane domain superfamily
365 549 SMART SM00382 AAA_5
365 549 InterPro IPR003593 AAA+ ATPase domain
41 61 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 322 FunFam G3DSA:1.20.1560.10:FF:000060 Cysteine/glutathione ABC transporter ATP-binding protein/permease CydC
26 287 Pfam PF00664 ABC transporter transmembrane region
26 287 InterPro IPR011527 ABC transporter type 1, transmembrane domain
133 155 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
331 573 FunFam G3DSA:3.40.50.300:FF:001297 Cysteine/glutathione ABC transporter ATP-binding protein/permease CydC
183 242 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
7 323 SUPERFAMILY SSF90123 ABC transporter transmembrane region
7 323 InterPro IPR036640 ABC transporter type 1, transmembrane domain superfamily
278 304 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
475 489 ProSitePatterns PS00211 ABC transporters family signature.
475 489 InterPro IPR017871 ABC transporter-like, conserved site
339 554 CDD cd03247 ABCC_cytochrome_bd
305 573 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
19 306 ProSiteProfiles PS50929 ABC transporter integral membrane type-1 fused domain profile.
19 306 InterPro IPR011527 ABC transporter type 1, transmembrane domain
267 277 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
36 40 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
13 569 PANTHER PTHR24222 ABC TRANSPORTER B FAMILY
13 569 InterPro IPR039421 Type 1 protein exporter
163 182 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
243 266 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
356 502 Pfam PF00005 ABC transporter
356 502 InterPro IPR003439 ABC transporter-like, ATP-binding domain
339 572 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile.
339 572 InterPro IPR003439 ABC transporter-like, ATP-binding domain
1 15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
158 162 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
325 572 Gene3D G3DSA:3.40.50.300 -
325 572 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
160 182 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
62 136 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
280 302 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
16 35 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
333 570 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
333 570 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
16 38 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
6 533 NCBIfam TIGR02868 thiol reductant ABC exporter subunit CydC
6 533 InterPro IPR014223 Glutathione/L-cysteine transport system ATP-binding/permease protein CydC/D
243 265 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
48 70 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; 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 #35
0.904
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Surrounding area
Site 2 FPocket #49
0.637
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Surrounding area
Site 3 FPocket #45
0.306
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Surrounding area
Site 4 FPocket #18
0.247
Likely same site as P2Rank 1 0.4 Å 8 shared residues 100% 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
0.324
Likely same site as FPocket 18 0.4 Å 8 shared residues 100% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.2
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Surrounding area
Site 3 P2Rank #3
0.191
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Surrounding area
Site 4 P2Rank #4
0.123
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Surrounding area
Site 5 P2Rank #5
0.035
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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_A0A0H3GUY5
AlphaFold DB full sequence Viewing
ColabFold KP13_04219
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.

54 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ANP PDB via homolog 506.2 Da · LogP -2.06 · TPSA 281.9 Open detail RCSB PDB
GSH PDB via homolog Detail RCSB PDB
O34 PDB via homolog Detail RCSB PDB
Z5G PDB via homolog Detail RCSB PDB
ZINC2922863 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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
ANP RCSB PDB 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)…
GSH RCSB PDB P40416 307.3 Da LogP -2.21 TPSA 158.8 1 viol. ✓ Clean C(CC(=O)N[C@@H](CS)C(=O)NCC(=O)O)[C@@H](C(=O)O)N
O34 RCSB PDB Q1RAG3 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…
Z5G RCSB PDB A0A0B9X4I2 335.8 Da LogP 4.23 TPSA 66.4 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)Nc2c(c3c(s2)CCCC3)C(=O)O)Cl

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.