KpKP13 Protein target profile

putative nicotinate-nucleotide adenylyltransferase

Accession: KP13_03335

Gene: AHE45714.1 nadD 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GLD7
Length 216
Pocket druggability (P2Rank · AlphaFold DB model) 0.968
Direct ligand evidence 0 57 total records
Functional annotation 1 EC 6 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 (%)
26.695 Lower values reduce human off-target concern.
Human E-value
1.19e-06
Gut microbiome similarity
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
75.472 Higher values support similarity to known essential genes.
DEG E-value
3.64e-123 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
92.71 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) 0.968
Structure A0A0H3GLD7
Pocket Pocket 1
Druggability (FPocket) 0.492
Structure A0A0H3GLD7
Pocket Pocket 8
ColabFold model
P2Rank 0.961 · Pocket 1
FPocket 0.044 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 112 / 4744 genomes with a hit
Prevalence 2.4%

Sequence

Primary amino-acid sequence viewer.

MVDMTQLQAIYGGTFDPVHYGHLKPVEILANQIGLSKVIIMPNNVPPHRPQPEATSAQRVHMLKLAIADKPLFTLDERELRRDTPSWTAQTLQEWRQEQGPRKPLAFIIGQDSLLTFPTWHNYETILDNVHLIVCRRPGYPLTMAQEADQRWLDRHLTHDVESLHNRPSGVIYLAETPWFDISATIIRQRLERGESCDEMLPAAVLDYIREQGLYC

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0016779 Catalysis of the transfer of a nucleotidyl group from one compound (donor) to another (acceptor).
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
  • GO:0009435 The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD+), a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions. NAD+ is derived from various sources including vitamin B3.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0004515 Catalysis of the reaction: nicotinate beta-D-ribonucleotide + ATP + H+ = deamido-NAD+ + diphosphate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
10 190 Pfam PF01467 Cytidylyltransferase-like
10 190 InterPro IPR004821 Cytidyltransferase-like domain
10 215 NCBIfam TIGR00482 nicotinate (nicotinamide) nucleotide adenylyltransferase
10 215 InterPro IPR005248 Nicotinate/nicotinamide nucleotide adenylyltransferase
9 71 NCBIfam TIGR00125 cytidyltransferase-like domain
9 71 InterPro IPR004821 Cytidyltransferase-like domain
6 216 Hamap MF_00244 Probable nicotinate-nucleotide adenylyltransferase [nadD].
6 216 InterPro IPR005248 Nicotinate/nicotinamide nucleotide adenylyltransferase
9 215 CDD cd02165 NMNAT
9 215 InterPro IPR005248 Nicotinate/nicotinamide nucleotide adenylyltransferase
7 215 SUPERFAMILY SSF52374 Nucleotidylyl transferase
7 215 PANTHER PTHR39321 NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE-RELATED
7 215 InterPro IPR005248 Nicotinate/nicotinamide nucleotide adenylyltransferase
5 215 Gene3D G3DSA:3.40.50.620 HUPs
5 215 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
5 216 FunFam G3DSA:3.40.50.620:FF:000039 Probable nicotinate-nucleotide adenylyltransferase

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

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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
0.968
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
0.492
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_A0A0H3GLD7
AlphaFold DB full sequence Viewing
ColabFold KP13_03335
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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
DND PDB via homolog 665.4 Da · LogP -2.42 · TPSA 312.5 Open detail RCSB PDB
E9A PDB via homolog Detail RCSB PDB
JJZ PDB via homolog Detail RCSB PDB
KJZ PDB via homolog Detail RCSB PDB
LJZ 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
DND RCSB PDB P54455 665.4 Da LogP -2.42 TPSA 312.5 3 viol. ✓ Clean c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(…
E9A RCSB PDB P9WJJ5 435.6 Da LogP 5.05 TPSA 44.3 1 viol. ✓ Clean C[C@H]1CC[C@@H]([C@@H](C1)OC(=O)C[n+]2c3ccccc3n…
JJZ RCSB PDB C3L5T6 429.9 Da LogP 5.52 TPSA 70.6 1 viol. ✓ Clean c1ccc2c(c1)cc3ccccc3c2C=NNC(=O)CCC(=O)Nc4cccc(c…
KJZ RCSB PDB C3L5T6 437.9 Da LogP 4.16 TPSA 99.1 ✓ Ro5 ✓ Clean c1ccc2c(c1)cccc2/C=N/N(CC(=O)O)C(=O)CCC(=O)Nc3c…
LJZ RCSB PDB C3L5T6 579.4 Da LogP 5.26 TPSA 141.8 2 viol. Alert c1cc(c(cc1)Cl)NC(=O)CCC(=O)/N=N/C=C2C=CC(=C/N=N…
NCN RCSB PDB Q9HX21 335.2 Da LogP -2.23 TPSA 160.5 ✓ Ro5 ✓ Clean c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P…
XE RCSB PDB P0A752 131.3 Da LogP 0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Xe]

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.