Protein target profile

KP13_00989

NADH-quinone oxidoreductase subunit F

Genome: KpKP13 Gene: AHE43481.1 nuoF 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H110
Length 445
Pocket druggability 0.769
Direct ligand evidence 0 70 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 (%)
54.135 Lower values reduce human off-target concern.
Human E-value
3.45e-42
Gut microbiome similarity
2.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
65.455 Higher values support similarity to known essential genes.
DEG E-value
1.6699999999999999e-180 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
93.05 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 0.769
Structure A0A0H3H110
Pocket Pocket 7
P2Rank 0.911
Structure A0A0H3H110
Pocket Pocket 1
ColabFold model
FPocket 0.365 · Pocket 26
P2Rank 0.904 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 134 / 4744 genomes with a hit
Prevalence 2.8%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MKTVIRTAETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGMAPDEIVTAVKDAGLKGRGGAGFSTGLKWSLMPKDESMNIRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAQHLRRAIAEATEAGLLGKNILGTGFDFELFVHTGAGRYICGEETALINSLEGRRANPRSKPPFPASSGVWGKPTCVNNVETLCNVPAILANGVEWYQNISTSKDAGTKLMGFSGRVKNPGVWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFLTEAHLDLPMEFESIGKAGSRLGTSLAMAVDHEINMVSLVRNLEEFFARESCGWCTPCRDGLPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAHAPGAVEPLQSAIKYFREEFEAGIKQQFSNTHAINGIQPNLLKTRW

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
  • GO:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0008137 Catalysis of the reaction: NADH + ubiquinone + 5 H+(in) = NAD+ + ubiquinol + 4 H+(out).
  • GO:0046872 Binding to a metal ion.
  • GO:0048038 Binding to a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
349 360 ProSitePatterns PS00645 Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2.
349 360 InterPro IPR001949 NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site
338 421 Pfam PF10589 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
338 421 InterPro IPR019575 NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain
336 381 SMART SM00928 NADH_4Fe_4S_2
336 381 InterPro IPR019575 NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain
240 332 Gene3D G3DSA:3.10.20.600 -
59 238 FunFam G3DSA:3.40.50.11540:FF:000001 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
13 423 NCBIfam TIGR01959 NADH-quinone oxidoreductase subunit NuoF
13 423 InterPro IPR011537 NADH ubiquinone oxidoreductase, F subunit
334 432 Gene3D G3DSA:1.20.1440.230 -
334 432 InterPro IPR037207 NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily
5 58 Gene3D G3DSA:6.10.250.1450 -
54 226 Pfam PF01512 Respiratory-chain NADH dehydrogenase 51 Kd subunit
54 226 InterPro IPR011538 NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain
8 426 PANTHER PTHR43578 NADH-QUINONE OXIDOREDUCTASE SUBUNIT F
59 238 Gene3D G3DSA:3.40.50.11540 -
59 238 InterPro IPR037225 NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily
174 189 ProSitePatterns PS00644 Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1.
174 189 InterPro IPR001949 NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site
241 332 FunFam G3DSA:3.10.20.600:FF:000002 NADH-quinone oxidoreductase subunit F
333 429 SUPERFAMILY SSF140490 Nqo1C-terminal domain-like
333 429 InterPro IPR037207 NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily
334 431 FunFam G3DSA:1.20.1440.230:FF:000002 NADH-quinone oxidoreductase subunit F
13 247 SUPERFAMILY SSF142019 Nqo1 FMN-binding domain-like
13 247 InterPro IPR037225 NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily
248 330 SUPERFAMILY SSF142984 Nqo1 middle domain-like

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 · FPocket

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

Site 1 FPocket #7
0.769
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.911
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.164
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.049
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.039
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.023
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:351-351
UniProt: Binding site:354-354
UniProt: Binding site:357-357
UniProt: Binding site:398-398
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_A0A0H3H110
AlphaFold DB full sequence Viewing
ColabFold KP13_00989
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
3PE PDB via homolog 748.1 Da · LogP 12.06 · TPSA 134.4 Open detail RCSB PDB
970 PDB via homolog Detail RCSB PDB
AYA PDB via homolog Detail RCSB PDB
CDL PDB via homolog Detail RCSB PDB
DCQ 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
3PE RCSB PDB W5PUX0 748.1 Da LogP 12.06 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC…
970 RCSB PDB W5PUX0 394.4 Da LogP 3.70 TPSA 63.2 ✓ Ro5 ✓ Clean CC(=C)[C@H]1Cc2c(ccc3c2O[C@@H]4COc5cc(c(cc5[C@@…
AYA RCSB PDB W5PUX0 131.1 Da LogP -0.40 TPSA 66.4 ✓ Ro5 ✓ Clean C[C@@H](C(=O)O)NC(=O)C
CDL RCSB PDB A0A4X1SZP7 1464.1 Da LogP 23.31 TPSA 242.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…
DCQ RCSB PDB W5PUX0 322.4 Da LogP 4.49 TPSA 52.6 ✓ Ro5 Alert CCCCCCCCCCC1=C(C(=O)C(=C(C1=O)OC)OC)C
FES RCSB PDB W5PUX0 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
FME RCSB PDB W5PUX0 177.2 Da LogP -0.06 TPSA 66.4 ✓ Ro5 ✓ Clean CSCC[C@@H](C(=O)O)NC=O
HQH RCSB PDB Q56222 415.6 Da LogP 5.05 TPSA 71.6 1 viol. ✓ Clean C/C=C(\C)/[C@@H]([C@H](C)/C=C(\C)/C=C/C/C(=C/CC…
HQK RCSB PDB Q56222 364.9 Da LogP 5.24 TPSA 34.9 1 viol. ✓ Clean CC(C)(C)c1ccc(cc1)CSC2=C(C(=O)N(N=C2)C(C)(C)C)Cl
HQW RCSB PDB Q56222 397.4 Da LogP 4.66 TPSA 91.8 ✓ Ro5 ✓ Clean CC1=C(OC(=C(C1=O)C)OC)[C@H]2C/C(=C/C(=C/c3ccc(c…
L3W RCSB PDB O66841 697.4 Da LogP -3.38 TPSA 354.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
MYR RCSB PDB W5PUX0 228.4 Da LogP 4.77 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCCCCCC(=O)O
PC1 RCSB PDB W5PUX0 790.2 Da LogP 12.17 TPSA 111.2 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])…
PEE RCSB PDB A0A4X1SZP7 744.0 Da LogP 11.61 TPSA 134.4 2 viol. ✓ Clean CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN…
PLX RCSB PDB A0A4X1SZP7 767.1 Da LogP 11.61 TPSA 114.7 2 viol. ✓ Clean CCCCCCCCCCCCCCCCC[C@@H](O)O[C@H](CO[C@@H](CCCCC…
PNS RCSB PDB W5PUX0 358.4 Da LogP -0.96 TPSA 145.2 1 viol. ✓ Clean CC(C)(COP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
SMA RCSB PDB Q56222 514.7 Da LogP 6.14 TPSA 87.4 2 viol. ✓ Clean C/C=C(\C)/C=C/C=C[C@@H]([C@@H](C)[C@H]([C@@H](C…
UQ1 RCSB PDB Q56222 250.3 Da LogP 2.32 TPSA 52.6 ✓ Ro5 Alert CC1=C(C(=O)C(=C(C1=O)OC)OC)CC=C(C)C
UQ2 RCSB PDB P25708 318.4 Da LogP 4.04 TPSA 52.6 ✓ Ro5 Alert CC1=C(C(=O)C(=C(C1=O)OC)OC)C\C=C(/C)\CCC=C(C)C
ZMP RCSB PDB A0A4X1SZP7 568.7 Da LogP 4.07 TPSA 162.3 1 viol. ✓ Clean CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](C(C)(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.