KpKP13 Protein target profile

Cytidylate kinase

Accession: KP13_31499

Gene: AHE45430.1 cmk 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GL15
Length 227
Pocket druggability (P2Rank · AlphaFold DB model) 0.926
Direct ligand evidence 0 53 total records
Functional annotation 1 EC 8 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
No hit
Gut microbiome similarity
4.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
90.308 Higher values support similarity to known essential genes.
DEG E-value
2.19e-150 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
93.15 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) 0.926
Structure A0A0H3GL15
Pocket Pocket 1
Druggability (FPocket) 0.592
Structure A0A0H3GL15
Pocket Pocket 5
ColabFold model
P2Rank 0.901 · Pocket 1
FPocket 0.581 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 217 / 4744 genomes with a hit
Prevalence 4.6%

Sequence

Primary amino-acid sequence viewer.

MTANIPVITIDGPGGAGKGTLCKAMAEALGWHLLDSGAIYRVLALAALHHHVDVESEEALVPMAAHLDVRFISTDGNLEVVLEGEDVSSEIRTQEVANAASKVAAFPRVREALLRRQRAFRELPGLIADGRDMGTVVFPDAPVKIFLDASADERAHRRMRQLQEKGFDVNFERLLSEIKERDDRDRNRAVAPLVPAADALVLDSTELNIEQVIEKALQYAREKLAVA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0004127 OBSOLETE. Catalysis of the reaction: ATP + (d)CMP = ADP + (d)CDP.
  • GO:0006139 Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0036430 Catalysis of the reaction: ATP + CMP = ADP + CDP.
  • GO:0036431 Catalysis of the reaction: ATP + dCMP = ADP + dCDP.
  • GO:0015949 The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
  • GO:0006220 The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
7 205 CDD cd02020 CMPK
7 205 InterPro IPR011994 Cytidylate kinase domain
1 227 Gene3D G3DSA:3.40.50.300 -
1 227 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
4 215 PANTHER PTHR21299 CYTIDYLATE KINASE/PANTOATE-BETA-ALANINE LIGASE
8 221 Pfam PF02224 Cytidylate kinase
8 221 InterPro IPR011994 Cytidylate kinase domain
6 224 Hamap MF_00238 Cytidylate kinase [cmk].
6 224 InterPro IPR003136 Cytidylate kinase
202 222 Coils Coil Coil
1 227 FunFam G3DSA:3.40.50.300:FF:000262 Cytidylate kinase
6 224 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
6 224 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
6 219 NCBIfam TIGR00017 (d)CMP kinase
6 219 InterPro IPR003136 Cytidylate 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.

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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 · P2Rank

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

Pocket 1 P2Rank #1
0.926
Likely same site as FPocket 1 0.9 Å 29 shared residues 94% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.003
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #5
0.592
Show in viewer
Surrounding area
Pocket 2 FPocket #1
0.402 Unusual size
Likely same site as P2Rank 1 0.9 Å 29 shared residues 94% of smaller site
Show in viewer
Surrounding area
Pocket 3 FPocket #13
0.377
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Surrounding area
Residue sets
UniProt: Binding site:27-35
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_A0A0H3GL15
AlphaFold DB full sequence Viewing
ColabFold KP13_31499
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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
CAR PDB via homolog 323.2 Da · LogP -2.45 · TPSA 177.4 Open detail RCSB PDB
DC PDB via homolog Detail RCSB PDB
DOC PDB via homolog Detail RCSB PDB
ZINC12503923 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC12503924 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
CAR RCSB PDB P0A6I0 323.2 Da LogP -2.45 TPSA 177.4 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2[C@H]([C@@H]([C@H](O2)CO…
DC RCSB PDB P0A6I0 307.2 Da LogP -1.42 TPSA 157.1 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O…
DOC RCSB PDB P0A6I0 291.2 Da LogP -0.39 TPSA 136.9 ✓ Ro5 ✓ Clean C1C[C@@H](O[C@@H]1COP(=O)(O)O)N2C=CC(=NC2=O)N

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.

Cross-references

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