Protein target profile

KP13_04342

Protein clpV1

Genome: KpKP13 Gene: AHE44926.1 clpV1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSF4
Length 884
Pocket druggability 0.394
Direct ligand evidence 0 56 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
Human identity (%)
35.776 Lower values reduce human off-target concern.
Human E-value
1.74e-39
Gut microbiome similarity
1.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
84.67 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 0.394
Structure A0A0H3GSF4
Pocket Pocket 15
P2Rank 0.636
Structure A0A0H3GSF4
Pocket Pocket 1
ColabFold model
FPocket 0.5 · Pocket 59
P2Rank 0.67 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 61 / 4744 genomes with a hit
Prevalence 1.3%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MENPASLLRRLNPCCARAMEGAASLCQTRAHAEILPEHWLLKLLEQGEGDLTVLARRYEWDMDALWQDLLSWLDKQPRSVRHRPQLSDHTLRLMQEAWLIASLSGEAQIRSVHLLMALVEKQNLIQCDGLWPLLTLGQRQLERLRPLLDAQSDERPPAQQEAALAQPHGGDVEFVGRPAGSELNADGLNPALQNALDKFTLDVTAKARDGLIDPVFGRDTEIRQMVDILSRRRKNNPILVGEPGVGKTALVEGLALRIAEGNVPDALKPVSVRTLDLGLLQAGAGVKGEFEQRLKNIIEAVQQSPSPVLLFIDEAHTIIGAGNQAGGADAANLLKPALARGELRTIAATTWSEYKQYFERDAALERRFQMVKVDEPDDDTACLMLRGLKSRYADHHGVHITDDAVRAAVTLSRRYLTGRQLPDKAVDLLDTASARLRMSLDTVPEPLTRMKAQLTALAMEKQALLEDIALGNSARGDRLADIEQEEIRLILALDTLETQYGQELQLTEALLACRRDISRQAEINDLQNALIAVQQGNPLLGLDVDVRTVATVIADWTGVPLSSLMKDEQTELLSLEESLGKRVVGQEAALSAIARRLRAAKTGLTPENGPQGVFLLVGPSGTGKTETALALADALFGGEKALITINLSEYQEPHTVSQLKGSPPGYVGYGQGGILTEAVRKRPYSVVLLDEVEKAHRDVMNLFYQVFDRGVMRDGEGREIDFRNTVILMTANLGSDLLMQLLDEQPEASESDLHELLRPVLRGHFQPALLARFQTVIYRPLPAAALRAIVGMKLGQVSQRLACHYGITTTLSESLFDALTEACLLPDTGARNVDSLLNQQILPALSQQLLSHMAAGQKPRQVTLGYHEEEGVVMAFDEGTISDE

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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0008233 Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
  • GO:0034605 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

52 records
Show feature table
Start End DB Term Name
216 376 CDD cd00009 AAA
11 864 NCBIfam TIGR03345 type VI secretion system ATPase TssH
11 864 InterPro IPR017729 AAA+ ATPase ClpV1
479 499 Coils Coil Coil
572 778 CDD cd19499 RecA-like_ClpB_Hsp104-like
329 341 ProSitePatterns PS00870 Chaperonins clpA/B signature 1.
329 341 InterPro IPR018368 ClpA/B, conserved site 1
563 779 FunFam G3DSA:3.40.50.300:FF:000025 ATP-dependent Clp protease subunit
188 377 Gene3D G3DSA:3.40.50.300 -
188 377 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
781 877 Gene3D G3DSA:1.10.8.60 -
610 783 SMART SM00382 AAA_5
610 783 InterPro IPR003593 AAA+ ATPase domain
233 378 SMART SM00382 AAA_5
233 378 InterPro IPR003593 AAA+ ATPase domain
447 467 Coils Coil Coil
13 124 SUPERFAMILY SSF81923 Double Clp-N motif
13 124 InterPro IPR036628 Clp, N-terminal domain superfamily
194 518 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
194 518 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
8 157 ProSiteProfiles PS51903 Clp repeat (R) domain profile.
8 157 InterPro IPR004176 Clp, repeat (R) domain
559 852 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
559 852 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
379 557 Gene3D G3DSA:3.40.50.300 -
379 557 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
783 855 Pfam PF10431 C-terminal, D2-small domain, of ClpB protein
783 855 InterPro IPR019489 Clp ATPase, C-terminal
15 857 PANTHER PTHR11638 ATP-DEPENDENT CLP PROTEASE
238 350 Pfam PF00004 ATPase family associated with various cellular activities (AAA)
238 350 InterPro IPR003959 ATPase, AAA-type, core
1 158 Gene3D G3DSA:1.10.1780.10 -
1 158 InterPro IPR036628 Clp, N-terminal domain superfamily
610 775 Pfam PF07724 AAA domain (Cdc48 subfamily)
610 775 InterPro IPR003959 ATPase, AAA-type, core
614 632 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature
614 632 InterPro IPR001270 ClpA/B family
688 706 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature
688 706 InterPro IPR001270 ClpA/B family
659 677 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature
659 677 InterPro IPR001270 ClpA/B family
721 735 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature
721 735 InterPro IPR001270 ClpA/B family
378 468 Pfam PF17871 AAA lid domain
378 468 InterPro IPR041546 ClpA/ClpB, AAA lid domain
22 65 Pfam PF02861 Clp amino terminal domain, pathogenicity island component
22 65 InterPro IPR004176 Clp, repeat (R) domain
186 377 FunFam G3DSA:3.40.50.300:FF:000010 Chaperone clpB 1, putative
781 873 SMART SM01086 ClpB_D2_small_2
781 873 InterPro IPR019489 Clp ATPase, C-terminal
562 778 Gene3D G3DSA:3.40.50.300 -
562 778 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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 #15
0.394
Likely same site as P2Rank 2 3.1 Å 20 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.636
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.527
Likely same site as FPocket 15 3.1 Å 20 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.175
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.124
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.086
Show in viewer
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_A0A0H3GSF4
AlphaFold DB full sequence Viewing
ColabFold KP13_04342
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.

56 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 6 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 0 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
AGS PDB via homolog Detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
MNT PDB via homolog Detail RCSB PDB
RPI PDB via homolog Detail RCSB PDB

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 Q9RA63 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)…
AGS RCSB PDB E0J719 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 RCSB PDB Q9RA63 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)…
MNT RCSB PDB Q9RA63 544.4 Da LogP 1.19 TPSA 230.5 2 viol. ✓ Clean CNc1ccccc1C(=O)O[C@H]2C[C@@H](O[C@@H]2CO[P@](=O…
RPI RCSB PDB P37571 254.2 Da LogP -1.61 TPSA 168.8 1 viol. ✓ Clean [H]/N=C(/NCCC[C@@H](C(=O)O)N)\NP(=O)(O)O
SRT RCSB PDB P37571 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@H]([C@H](C(=O)O)O)(C(=O)O)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.