Protein target profile

VK055_2560

chaperone protein DnaK

Genome: KpATCC43816 Gene: AIK81157.1 dnaK 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GN02
Length 638
Pocket druggability 0.425
Direct ligand evidence 0 170 total records
Functional annotation 0 EC 5 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 (%)
65.873 Lower values reduce human off-target concern.
Human E-value
4.4599999999999996e-54
Gut microbiome similarity
83.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
97.492 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
88.39 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 0.425
Structure A0A0H3GN02
Pocket Pocket 25
P2Rank 0.923
Structure A0A0H3GN02
Pocket Pocket 1
ColabFold model
FPocket 0.746 · Pocket 5
P2Rank 0.943 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 3970 / 4744 genomes with a hit
Prevalence 83.7%

Cross-references

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

Chemistry

ChEMBL DWT ChEMBL DXH ChEMBL CHEMBL462871 ChEMBL CHEMBL470334 ChEMBL EAM ChEMBL CHEMBL5414287 ChEMBL GB8 ChEMBL CHEMBL473972 ChEMBL CHEMBL3576921 ChEMBL CHEMBL4649247 ChEMBL CHEMBL502775 ChEMBL CHEMBL5431926 ChEMBL CHEMBL4646130 ChEMBL CHEMBL1481974 ChEMBL CHEMBL7075 ChEMBL CHEMBL471004 ChEMBL CHEMBL5639838 ChEMBL CHEMBL4639280 ChEMBL CHEMBL4648396 ChEMBL CHEMBL5419391 ChEMBL REF ChEMBL CHEMBL538168 ChEMBL 3BK ChEMBL CHEMBL1784882 ChEMBL B1T ChEMBL BHQ ChEMBL CHEMBL1173145 ChEMBL CHEMBL1173146 ChEMBL CHEMBL1256759 ChEMBL CHEMBL1304172 ChEMBL CHEMBL1304794 ChEMBL CHEMBL1306822 ChEMBL CHEMBL1321399 ChEMBL CHEMBL1338243 ChEMBL CHEMBL1338249 ChEMBL CHEMBL1340133 ChEMBL CHEMBL1354360 ChEMBL CHEMBL1356609 ChEMBL CHEMBL1364096 ChEMBL CHEMBL1367586 ChEMBL CHEMBL1372914 ChEMBL CHEMBL1372915 ChEMBL CHEMBL1377193 ChEMBL CHEMBL1379018 ChEMBL CHEMBL1383226 ChEMBL CHEMBL1385229 ChEMBL CHEMBL1391956 ChEMBL CHEMBL1420416 ChEMBL CHEMBL1435062 ChEMBL CHEMBL1437480 ChEMBL CHEMBL1447817 ChEMBL CHEMBL1451305 ChEMBL CHEMBL1452370 ChEMBL CHEMBL1452612 ChEMBL CHEMBL1454693 ChEMBL CHEMBL1463707 ChEMBL CHEMBL1468959 ChEMBL CHEMBL1475620 ChEMBL CHEMBL1484765 ChEMBL CHEMBL1486792 ChEMBL CHEMBL1492346 ChEMBL CHEMBL1501824 ChEMBL CHEMBL1506967 ChEMBL CHEMBL1507872 ChEMBL CHEMBL1511994 ChEMBL CHEMBL1513351 ChEMBL CHEMBL1514542 ChEMBL CHEMBL1531194 ChEMBL CHEMBL1532354 ChEMBL CHEMBL1532863 ChEMBL CHEMBL1536258 ChEMBL CHEMBL1549548 ChEMBL CHEMBL1556958 ChEMBL CHEMBL1557422 ChEMBL CHEMBL1566858 ChEMBL CHEMBL1570312 ChEMBL CHEMBL1575634 ChEMBL CHEMBL1583245 ChEMBL CHEMBL1592886 ChEMBL CHEMBL1593896 ChEMBL CHEMBL1599138 ChEMBL CHEMBL1610955 ChEMBL CHEMBL1702170 ChEMBL CHEMBL1705084 ChEMBL CHEMBL1705507 ChEMBL CHEMBL1709225 ChEMBL CHEMBL1726711 ChEMBL CHEMBL1728587 ChEMBL CHEMBL1730236 ChEMBL CHEMBL1730338 ChEMBL CHEMBL1876990 ChEMBL CHEMBL1887807 ChEMBL CHEMBL1980588 ChEMBL CHEMBL1986032 ChEMBL CHEMBL1986073 ChEMBL CHEMBL1991885 ChEMBL CHEMBL1993431 ChEMBL CHEMBL3765259 ChEMBL CHEMBL4450771 ChEMBL CHEMBL524376

Sequence

Primary amino-acid sequence viewer.

MGKIIGIDLGTTNSCVAIMDGTTARVLENAEGDRTTPSIIAYTQDGETLVGQPAKRQAVTNPQNTLFAIKRLIGRRFQDEEVQRDVSIMPYKIVAADNGDAWLDVKGTKTAPPQISAEVLKKMKKTAEDYLGEPVTEAVITVPAYFNDAQRQATKDAGRIAGLEVKRIINEPTAAALAYGLDKEVGNRTIAVYDLGGGTFDISIIEIDEVDGEKTFEVLATNGDTHLGGEDFDTRLINYLVDEFKKDQGIDLRNDPLAMQRLKEAAEKAKIELSSAQQTDVNLPYITADATGPKHMNIKVTRAKLESLVEDLVNRSIEPLKVALQDAGLSVSDINDVILVGGQTRMPMVQKKVAEFFGKEPRKDVNPDEAVAIGAAVQGGVLTGDVKDVLLLDVTPLSLGIETMGGVMTALISKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRASDNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEEEIQKMVREAEANAESDRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALESSLKGEDKADIEAKMQALAQASQKLMEIAQQQHAQQQAGSADAQASNAKDDDVVDAEFEEVKDKK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0006457 The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0140662 Binding to a protein or a protein-containing complex to assist the protein folding process, driven by ATP hydrolysis.
  • GO:0051082 Binding to an unfolded protein.
  • GO:0051087 Binding to a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

47 records
Show feature table
Start End DB Term Name
599 638 MobiDBLite mobidb-lite consensus disorder prediction
584 604 Coils Coil Coil
192 205 ProSitePatterns PS00329 Heat shock hsp70 proteins family signature 2.
192 205 InterPro IPR018181 Heat shock protein 70, conserved site
5 192 FunFam G3DSA:3.30.420.40:FF:000004 Molecular chaperone DnaK
507 608 FunFam G3DSA:1.20.1270.10:FF:000001 Molecular chaperone DnaK
4 602 Pfam PF00012 Hsp70 protein
4 602 InterPro IPR013126 Heat shock protein 70 family
384 539 SUPERFAMILY SSF100920 Heat shock protein 70kD (HSP70), peptide-binding domain
384 539 InterPro IPR029047 Heat shock protein 70kD, peptide-binding domain superfamily
229 316 FunFam G3DSA:3.90.640.10:FF:000003 Molecular chaperone DnaK
507 602 SUPERFAMILY SSF100934 Heat shock protein 70kD (HSP70), C-terminal subdomain
507 602 InterPro IPR029048 Heat shock protein 70kD, C-terminal domain superfamily
378 561 FunFam G3DSA:2.60.34.10:FF:000014 Chaperone protein DnaK HSP70
518 561 MobiDBLite mobidb-lite consensus disorder prediction
259 279 Coils Coil Coil
381 506 Gene3D G3DSA:2.60.34.10 Substrate Binding Domain Of DNAk; Chain A, domain 1
381 506 InterPro IPR029047 Heat shock protein 70kD, peptide-binding domain superfamily
4 183 SUPERFAMILY SSF53067 Actin-like ATPase domain
4 183 InterPro IPR043129 ATPase, nucleotide binding domain
7 14 ProSitePatterns PS00297 Heat shock hsp70 proteins family signature 1.
7 14 InterPro IPR018181 Heat shock protein 70, conserved site
469 485 PRINTS PR00301 70kDa heat shock protein signature
138 158 PRINTS PR00301 70kDa heat shock protein signature
198 208 PRINTS PR00301 70kDa heat shock protein signature
31 43 PRINTS PR00301 70kDa heat shock protein signature
54 62 PRINTS PR00301 70kDa heat shock protein signature
334 350 PRINTS PR00301 70kDa heat shock protein signature
3 16 PRINTS PR00301 70kDa heat shock protein signature
388 407 PRINTS PR00301 70kDa heat shock protein signature
365 385 PRINTS PR00301 70kDa heat shock protein signature
180 366 Gene3D G3DSA:3.30.420.40 -
5 379 Gene3D G3DSA:3.30.420.40 -
1 634 Hamap MF_00332 Chaperone protein DnaK [dnaK].
1 634 InterPro IPR012725 Chaperone DnaK
3 603 NCBIfam TIGR02350 molecular chaperone DnaK
3 603 InterPro IPR012725 Chaperone DnaK
229 316 Gene3D G3DSA:3.90.640.10 Actin; Chain A, domain 4
507 607 Gene3D G3DSA:1.20.1270.10 -
507 607 InterPro IPR029048 Heat shock protein 70kD, C-terminal domain superfamily
599 617 MobiDBLite mobidb-lite consensus disorder prediction
187 382 SUPERFAMILY SSF53067 Actin-like ATPase domain
187 382 InterPro IPR043129 ATPase, nucleotide binding domain
337 351 ProSitePatterns PS01036 Heat shock hsp70 proteins family signature 3.
337 351 InterPro IPR018181 Heat shock protein 70, conserved site
5 569 PANTHER PTHR19375 HEAT SHOCK PROTEIN 70KDA
5 569 InterPro IPR013126 Heat shock protein 70 family

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 #25
0.425
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.923
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.286
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.242
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.212
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.204
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_A0A0H3GN02
AlphaFold DB full sequence Viewing
ColabFold VK055_2560
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.

170 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 120 records from similar proteins
Structural ligands 20 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3BH PDB via homolog 282.3 Da · LogP -2.40 · TPSA 165.6 Open detail RCSB PDB
3FD PDB via homolog Detail RCSB PDB
5P7 PDB via homolog Detail RCSB PDB
7DD PDB via homolog Detail RCSB PDB
7DT 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
3BH RCSB PDB P11021 282.3 Da LogP -2.40 TPSA 165.6 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(c(n2)N)[C@H]3[C@@H]([C@@H]([C@H](…
3FD RCSB PDB P11021 556.4 Da LogP 3.04 TPSA 164.4 2 viol. ✓ Clean c1cc(ccc1COCC2C(C(C(O2)n3c4c(c(ncn4)N)nc3NCc5cc…
5P7 RCSB PDB P0DMV8 275.3 Da LogP 0.14 TPSA 98.5 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(ncn2)N[C@@H]3C[C@@H]([C@H]([C@H]3O…
7DD RCSB PDB P11021 426.2 Da LogP -1.14 TPSA 219.7 2 viol. ✓ Clean c1cn(c2c1c(ncn2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)…
7DT RCSB PDB P11021 506.2 Da LogP -1.02 TPSA 266.2 3 viol. ✓ Clean c1cn(c2c1c(ncn2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ACP RCSB PDB P11021 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)…
ADN RCSB PDB P0DMV8 267.2 Da LogP -1.98 TPSA 139.5 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP RCSB PDB P47547 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)…
DAT RCSB PDB P11021 411.2 Da LogP -0.72 TPSA 212.4 1 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@]…
DTP RCSB PDB P11021 491.2 Da LogP -0.60 TPSA 258.9 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@]…
DTV RCSB PDB P0DMV8 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@H]([C@@H](CS)O)O)S
FLC RCSB PDB P0DMV8 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
GBA RCSB PDB P11021 346.1 Da LogP -1.22 TPSA 139.5 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(c(n2)Br)[C@H]3[C@@H]([C@@H]([C@H]…
H5V RCSB PDB P11021 280.3 Da LogP -0.98 TPSA 126.7 ✓ Ro5 ✓ Clean C[C@]1([C@@H]([C@H](O[C@H]1n2ccc3c2ncnc3N)CO)O)O
HFY RCSB PDB P11021 406.8 Da LogP 0.29 TPSA 151.6 ✓ Ro5 ✓ Clean c1ccc(c(c1)CNc2nc3c(ncnc3n2[C@H]4[C@@H]([C@@H](…
KC7 RCSB PDB P0DMV8 381.4 Da LogP 1.72 TPSA 107.7 ✓ Ro5 ✓ Clean c1ccc(cc1)COc2cccc3c2c(ncn3)N[C@@H]4C[C@@H]([C@…
NO7 RCSB PDB P38646 465.3 Da LogP -1.28 TPSA 218.6 2 viol. ✓ Clean C#CCNc1c2c(ncn1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=…
SGV RCSB PDB P0DMV8 309.3 Da LogP -2.28 TPSA 169.7 ✓ Ro5 ✓ Clean c1c(c2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)…
TEW RCSB PDB P0DMV8 [O-]=[W]123(O[W]45(=O)(O1[Te]6789O2[W]1(=O)(O3)…
TI8 RCSB PDB P0DMV8 488.9 Da LogP 1.80 TPSA 157.6 1 viol. ✓ Clean C=CC(=O)OCCC[C@@H]1[C@H]([C@H]([C@@H](O1)n2c3c(…

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.