Genome KpKP13

Protein target profile

Pantothenate kinase

Accession: KP13_01350

Gene: AHE46948.1 coaA 3D evidence: AlphaFold DB model + ColabFold model UniProt W8UTI4
Length 332
Pocket druggability (P2Rank · AlphaFold DB model) 0.977
Direct ligand evidence 0 70 total records
Functional annotation 1 EC 5 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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
No hit
Gut microbiome similarity
4.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
89.26 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.977
Structure W8UTI4
Pocket Pocket 1
Druggability (FPocket) 0.907
Structure W8UTI4
Pocket Pocket 8
ColabFold model
P2Rank 0.958 · Pocket 1
FPocket 0.497 · Pocket 7
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 205 / 4744 genomes with a hit
Prevalence 4.3%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MKHHRFKVFGDSKNMLMSQKEQTLMTPYLQFNRHQWAALRDSVPMTLTEEEITRLKGINEDLSLEEVAEIYLPLSRLLNFYISSNLRRQAVLEQFLGTNGQRIPYIISIAGSVAVGKSTTARVLQALLSRWPEHRHVELITTDGFLHPNSVLKERGLMKKKGFPQSYDMHRLVKFVSDLKSGVPQATAPVYSHLIYDVIPNGDKTVAQPDILILEGLNVLQSGMDYPHDPHHVFVSDFVDFSIYVDAPEELLKSWYINRFLKFREGAFTDPDSYFHNYAKLSKEEAVDIATSLWNEINLMNLKENILPTRERASLIMTKSANHSVNQVRLRK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0015937 The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
  • GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
  • GO:0004594 Catalysis of the reaction: ATP + pantothenate = ADP + D-4'-phosphopantothenate.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
106 330 CDD cd02025 PanK
106 330 InterPro IPR004566 Pantothenate kinase
18 332 FunFam G3DSA:3.40.50.300:FF:000242 Pantothenate kinase
14 332 Gene3D G3DSA:3.40.50.300 -
14 332 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
26 331 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
26 331 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
96 318 PANTHER PTHR10285 URIDINE KINASE
1 332 Hamap MF_00215 Pantothenate kinase [coaA].
1 332 InterPro IPR004566 Pantothenate kinase
17 332 PIRSF PIRSF000545 Pantothenate_kin
17 332 InterPro IPR004566 Pantothenate kinase
25 332 NCBIfam TIGR00554 type I pantothenate kinase
25 332 InterPro IPR004566 Pantothenate kinase
106 260 Pfam PF00485 Phosphoribulokinase / Uridine kinase family
106 260 InterPro IPR006083 Phosphoribulokinase/uridine kinase

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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.977
Likely same site as FPocket 8 0.3 Å 33 shared residues 92% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.024
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.022
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.005
Likely same site as FPocket 11 2.3 Å 7 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.004
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #8
0.907 Unusual size
Likely same site as P2Rank 1 0.3 Å 33 shared residues 92% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #11
0.34
Likely same site as P2Rank 4 2.3 Å 7 shared residues 100% of smaller site
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_W8UTI4
AlphaFold DB full sequence Viewing
ColabFold KP13_01350
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.

70 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 20 records from similar proteins
Structural ligands 20 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
0JR PDB via homolog 309.4 Da · LogP -0.42 · TPSA 111.6 Open detail RCSB PDB
ACP PDB via homolog Detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
COK PDB via homolog Detail RCSB PDB
FLC 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
0JR RCSB PDB B5XYG3 309.4 Da LogP -0.42 TPSA 111.6 ✓ Ro5 ✓ Clean CC(C)(CO)[C@H](C(=O)NCCC(=O)NCc1cccnc1)O
ACP RCSB PDB P9WPA7 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 P0A6I3 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)…
COK RCSB PDB P9WPA7 843.7 Da LogP -1.22 TPSA 366.8 3 viol. ✓ Clean CC(C)(CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]…
FLC RCSB PDB P9WPA7 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
GCP RCSB PDB P9WPA7 521.2 Da LogP -2.22 TPSA 289.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
MV1 RCSB PDB P9WPA7 344.5 Da LogP 1.74 TPSA 98.7 ✓ Ro5 ✓ Clean CCCCCCCCCNC(=O)CCNC(=O)[C@H](C(C)(C)CO)O
MV2 RCSB PDB P9WPA7 205.3 Da LogP -1.14 TPSA 89.8 ✓ Ro5 ✓ Clean CC(C)(CO)[C@@H](C(=O)NCCCO)O
PAU RCSB PDB P0A6I3 219.2 Da LogP -1.04 TPSA 106.9 ✓ Ro5 ✓ Clean CC(C)(CO)[C@H](C(=O)NCCC(=O)O)O
PAZ RCSB PDB P9WPA7 299.2 Da LogP -0.93 TPSA 153.4 ✓ Ro5 ✓ Clean CC(C)(COP(=O)(O)O)[C@H](C(=O)NCCC(=O)O)O
PN4 RCSB PDB B5XYG3 288.4 Da LogP 0.18 TPSA 98.7 ✓ Ro5 ✓ Clean CCCCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO)O
SH2 RCSB PDB B5XYG3 366.4 Da LogP -0.04 TPSA 117.1 ✓ Ro5 ✓ Clean CC(C)(CO)[C@H](C(=O)NCCC(=O)NCCc1ccc2c(c1)OCO2)O
ZVS RCSB PDB P9WPA7 468.5 Da LogP 4.64 TPSA 69.0 ✓ Ro5 ✓ Clean C[C@@H](c1nnc(n1C)SCCOc2ccc(cc2)F)NC(=O)c3ccccc…
ZVT RCSB PDB P9WPA7 434.9 Da LogP 4.27 TPSA 69.0 ✓ Ro5 ✓ Clean C[C@@H](c1nnc(n1C)SCCOc2ccc(cc2)F)NC(=O)c3ccccc…
ZVU RCSB PDB P9WPA7 438.5 Da LogP 4.76 TPSA 59.8 ✓ Ro5 ✓ Clean C[C@@H](c1nnc(n1C)SCc2ccc(cc2)F)NC(=O)c3ccccc3C…
ZVV RCSB PDB P9WPA7 464.5 Da LogP 4.80 TPSA 69.0 ✓ Ro5 ✓ Clean Cc1ccccc1OCCSc2nnc(n2C)[C@H](C)NC(=O)c3ccccc3C(…
ZVW RCSB PDB P9WPA7 562.6 Da LogP 6.29 TPSA 69.0 2 viol. ✓ Clean C[C@@H](c1nnc(n1Cc2ccc(cc2)F)SCCOc3ccc(cc3)F)NC…
ZVX RCSB PDB P9WPA7 436.5 Da LogP 3.89 TPSA 69.0 ✓ Ro5 ✓ Clean C[C@@H](c1nnc(n1C)SCCOc2ccc(cc2)F)NC(=O)c3c(ccc…
ZVY RCSB PDB P9WPA7 428.5 Da LogP 3.41 TPSA 89.7 ✓ Ro5 ✓ Clean c1ccnc(c1)N2CCN(CC2)Cc3cc(ccc3c4ccc(cc4)C#N)OCC…
ZVZ RCSB PDB P9WPA7 441.5 Da LogP 3.07 TPSA 81.5 ✓ Ro5 ✓ Clean CNC(=O)COc1ccc(c(c1)CN2CCN(CC2)c3ccccn3)c4ccc(c…

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.