Protein target profile

HT085_RS00320

redox-regulated ATPase YchF

Genome: NZ_AP023069.1 Gene: WHOF_00064 NGO_0063 TUM19854C_00540 ychF engD N776_09005 ESCNG_350010 NGK_0087 E8M63_11580 WHOF_01981 3D evidence: AlphaFold DB model UniProt A0AA44ZGR4 UniProt Q5FAG0 UniProt A0A1D3HQQ6 UniProt B4RP09
Length 363
Direct ligand evidence 0 55 total records
Functional annotation 0 EC 6 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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
Gut microbiome off-target
Hit

Essentiality

Essential (DEG)
Y

Localization

Localization
Cytoplasmic

Binding-site evidence

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 Medium
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MSLKCGIVGLPNVGKSTLFNALTQSGIEAANYPFCTIEPNVGIVEVPDPRMAELAKIVNPQKMQPAIVEFVDIAGLVAGASKGEGLGNRFLANIRETDAIVNVVRCFDDDNIVHVSGKVDPIADIETIGTELALADLASVEKAIVREEKRARSGDKDAQKLVDLCKKLLPHLDEGKPVRSFGLDAEERALLKPLFLLTAKPAMYVGNVAEDGFENNPHLDRLKELAAKENAPVVAVCAAMESEIAELEDGEKAEFLAEMGLEEPGLNRLIRAGYDLLGLQTYFTAGVKEVRAWTIHKGDTAPQAAGVIHTDFERGFIRAQVIAYDDFVSLGGEAKAKEAGKMRVEGKEYVVQDGDVMHFLFNV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • 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:0005525 Binding to GTP, guanosine triphosphate.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0046872 Binding to a metal ion.
  • GO:0043023 Binding to a large ribosomal subunit.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

38 records
Show feature table
Start End DB Term Name
1 363 NCBIfam TIGR00092 redox-regulated ATPase YchF
1 363 InterPro IPR004396 Ribosome-binding ATPase YchF/Obg-like ATPase 1
3 301 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
3 301 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
1 363 PIRSF PIRSF006641 EngD
5 277 CDD cd01900 YchF
5 277 InterPro IPR041706 YchF, N-terminal
48 363 Gene3D G3DSA:3.10.20.30 -
48 363 InterPro IPR012675 Beta-grasp domain superfamily
279 359 SUPERFAMILY SSF81271 TGS-like
279 359 InterPro IPR012676 TGS-like
120 200 Gene3D G3DSA:1.10.150.300 -
120 200 InterPro IPR023192 TGS-like domain superfamily
87 105 PRINTS PR00326 GTP1/OBG GTP-binding protein family signature
87 105 InterPro IPR006073 GTP binding domain
5 25 PRINTS PR00326 GTP1/OBG GTP-binding protein family signature
5 25 InterPro IPR006073 GTP binding domain
70 85 PRINTS PR00326 GTP1/OBG GTP-binding protein family signature
70 85 InterPro IPR006073 GTP binding domain
26 44 PRINTS PR00326 GTP1/OBG GTP-binding protein family signature
26 44 InterPro IPR006073 GTP binding domain
4 278 Gene3D G3DSA:3.40.50.300 -
4 278 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
2 363 Hamap MF_00944 Ribosome-binding ATPase YchF [ychF].
2 363 InterPro IPR004396 Ribosome-binding ATPase YchF/Obg-like ATPase 1
277 361 CDD cd04867 TGS_YchF_OLA1
277 361 InterPro IPR013029 YchF, C-terminal domain
278 361 ProSiteProfiles PS51880 TGS domain profile.
278 361 InterPro IPR004095 TGS
1 362 PANTHER PTHR23305 OBG GTPASE FAMILY
5 116 Pfam PF01926 50S ribosome-binding GTPase
5 116 InterPro IPR006073 GTP binding domain
279 362 Pfam PF06071 Protein of unknown function (DUF933)
279 362 InterPro IPR013029 YchF, C-terminal domain
3 256 ProSiteProfiles PS51710 OBG-type guanine nucleotide-binding (G) domain profile.
3 256 InterPro IPR031167 OBG-type guanine nucleotide-binding (G) domain
113 200 FunFam G3DSA:1.10.150.300:FF:000001 Ribosome-binding ATPase YchF
266 362 FunFam G3DSA:3.10.20.30:FF:000001 Ribosome-binding ATPase YchF

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.

Loading 3D structure...

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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
0.607
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Surrounding area
Site 2 FPocket #2
0.229
Likely same site as P2Rank 5 3.3 Å 15 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
0.518
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Surrounding area
Site 2 P2Rank #2
0.469
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Surrounding area
Site 3 P2Rank #3
0.146
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Surrounding area
Site 4 P2Rank #4
0.123
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Surrounding area
Site 5 P2Rank #5
0.07
Likely same site as FPocket 2 3.3 Å 15 shared residues 100% of smaller site
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Surrounding area
All structural evidence 0 experimental · 1 predicted

Structural evidence

0 + 1

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 HT085_RS00320
AlphaFold DB full sequence Viewing

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.

55 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ACP PDB via homolog 505.2 Da · LogP -1.52 · TPSA 269.9 Open detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
G4P PDB via homolog Detail RCSB PDB
GNP PDB via homolog Detail RCSB PDB
DWT ChEMBL via homolog · pchembl 7.23 (~58.9 nM) Detail ChEMBL

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
ACP RCSB PDB Q9NTK5 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP RCSB PDB Q6Z1J6 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)…
G4P RCSB PDB P20964 603.2 Da LogP -2.22 TPSA 345.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
GNP RCSB PDB Q6Z1J6 522.2 Da LogP -2.76 TPSA 301.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…

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.