KpKP13 Protein target profile

NADH dehydrogenase-like protein

Accession: KP13_03955

Gene: AHE47467.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A218N2W5
Length 438
Pocket druggability (P2Rank · AlphaFold DB model) 0.867
Direct ligand evidence 0 61 total records
Functional annotation 1 EC 4 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
No hit
Gut microbiome similarity
0.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
43.192 Higher values support similarity to known essential genes.
DEG E-value
3.29e-114 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
89.0 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) 0.867
Structure A0A218N2W5
Pocket Pocket 1
Druggability (FPocket) 0.304
Structure A0A218N2W5
Pocket Pocket 29
ColabFold model
P2Rank 0.94 · Pocket 1
FPocket 0.691 · Pocket 12
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 16 / 4744 genomes with a hit
Prevalence 0.3%

Sequence

Primary amino-acid sequence viewer.

MVMVHFCDQKHHVVVIGAGFGGLSVVRELEEPGVSITIIDRSNHHLFQPLLYQVAGASLPSAEIAWPVRSLFRHREDVRTLMAEVQDVDTDSREVLLKDGSRIDYDTLVVATGATHAYFGHDEWEQFAPGLKNLDDATTLRARILSAFEQAENTTDPALRAAYQTFVIVGGGPTGVELSGTIAELARKTLKNDFRSIDPTETRIILVEAGQRLLTAFPESLSEYTRQSLEKLGVEVSFGQPVTECSAEGVVYGGQPLPAKTIIWAAGVTASPAARWLKTEADRAGRVIVGADLTLPLHPEIFVIGDTAAVTGEDGRMIPGIAPAAKQEGQYVAKLIQSRLKDEKPVLKPFRYRHQGNLATIGRGLAVVDMGRLKLRGAMAWWFWKIIHLYFLIGTRNRLSVAISWIWNHSIGYRGARIITGGKSPDPDKSAVHSRSEE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0006116 OBSOLETE. A metabolic process that results in the oxidation of reduced nicotinamide adenine dinucleotide, NADH, to the oxidized form, NAD+.
  • GO:0003954 Catalysis of the reaction: NADH + H+ + acceptor = NAD+ + reduced acceptor.
  • GO:0050136 Catalysis of the reaction: NADH + H+ + a quinone = NAD+ + a quinol.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
301 308 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
12 34 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
165 190 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
3 402 Gene3D G3DSA:3.50.50.100 -
12 329 Pfam PF07992 Pyridine nucleotide-disulphide oxidoreductase
12 329 InterPro IPR023753 FAD/NAD(P)-binding domain
10 217 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
10 217 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
13 32 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
165 183 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
105 123 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
164 342 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
164 342 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
9 413 PANTHER PTHR43706 NADH DEHYDROGENASE
9 413 InterPro IPR045024 Alternative NADH dehydrogenase

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
0.867
Likely same site as FPocket 29 6.2 Å 19 shared residues 79% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.839
Likely same site as FPocket 29 5.6 Å 23 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.632
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.566
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.075
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #29
0.304 Unusual size
Likely same site as P2Rank 2 5.6 Å 23 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_A0A218N2W5
AlphaFold DB full sequence Viewing
ColabFold KP13_03955
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.

61 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 11 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 6 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
4W0 PDB via homolog 427.4 Da · LogP 6.13 · TPSA 42.1 Open detail RCSB PDB
CXS PDB via homolog Detail RCSB PDB
HQO PDB via homolog Detail RCSB PDB
MLI PDB via homolog Detail RCSB PDB
TRT 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
4W0 RCSB PDB Q8I302 427.4 Da LogP 6.13 TPSA 42.1 1 viol. ✓ Clean CC1=C(Nc2cccc(c2C1=O)F)c3ccc(cc3)Cc4ccc(cc4)OC(…
CXS RCSB PDB Q8I302 221.3 Da LogP 1.19 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCCS(=O)(=O)O
HQO RCSB PDB F5L3B8 259.3 Da LogP 3.69 TPSA 47.2 ✓ Ro5 Alert CCCCCCCc1cc(c2ccccc2[n+]1[O-])O
MLI RCSB PDB Q2FZV7 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
TRT RCSB PDB Q8I302 352.5 Da LogP 4.46 TPSA 36.9 ✓ Ro5 ✓ Clean CC(C)(C)CC(C)(C)c1ccc(cc1)OCCOCCOCCOC

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.