Protein target profile

KP13_00992

NADH-quinone oxidoreductase subunit B

Genome: KpKP13 Gene: AHE43478.1 nuoB 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GVQ5
Length 224
Pocket druggability 0.79
Direct ligand evidence 0 67 total records
Functional annotation 1 EC 10 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 (%)
57.265 Lower values reduce human off-target concern.
Human E-value
5.01e-44
Gut microbiome similarity
3.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
44.97 Higher values support similarity to known essential genes.
DEG E-value
4.37e-49 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
94.7 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 0.79
Structure A0A0H3GVQ5
Pocket Pocket 8
P2Rank 0.126
Structure A0A0H3GVQ5
Pocket Pocket 1
ColabFold model
FPocket 0.944 · Pocket 5
P2Rank 0.016 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 178 / 4744 genomes with a hit
Prevalence 3.8%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MDYTLTRIDPNGENDRYPLQKQEIVTDPLEQEVNKSVYMGKLEHALHDMVNWGRKNSIWPYNFGLSCCYVEMVTSFTAVHDVARFGAEVLRASPRQADLMVVAGTCFTKMAPVIQRLYDQMLEPKWVISMGACANSGGMYDIYSVVQGVDKFIPVDVYIPGCPPRPEAYMQALMLLQESIGKERRPLSWVVGDQGVYRANMQSERERKRGERIAVTNLRTPDEI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • GO:0008137 Catalysis of the reaction: NADH + ubiquinone + 5 H+(in) = NAD+ + ubiquinol + 4 H+(out).
  • 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: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.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0045271 Respiratory chain complex I is an enzyme of the respiratory chain. It consists of several polypeptide chains and is L-shaped, with a horizontal arm lying in the membrane and a vertical arm that projects into the matrix. The electrons of NADH enter the chain at this complex.
  • GO:0005506 Binding to an iron (Fe) ion.
  • GO:0050136 Catalysis of the reaction: NADH + H+ + a quinone = NAD+ + a quinol.
  • GO:0009060 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
  • GO:0015990 The transport of protons against an electrochemical gradient, using energy from electron transport.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
41 190 PANTHER PTHR11995 NADH DEHYDROGENASE
148 164 ProSitePatterns PS01150 Respiratory-chain NADH dehydrogenase 20 Kd subunit signature.
148 164 InterPro IPR006138 NADH-ubiquinone oxidoreductase, 20 Kd subunit
24 192 Gene3D G3DSA:3.40.50.12280 -
68 174 Pfam PF01058 NADH ubiquinone oxidoreductase, 20 Kd subunit
68 174 InterPro IPR006137 NADH:ubiquinone oxidoreductase-like, 20kDa subunit
24 192 FunFam G3DSA:3.40.50.12280:FF:000002 NADH-quinone oxidoreductase subunit B
27 181 Hamap MF_01356 NAD(P)H-quinone oxidoreductase subunit K, chloroplastic [ndhK].
27 181 InterPro IPR006138 NADH-ubiquinone oxidoreductase, 20 Kd subunit
46 182 NCBIfam TIGR01957 NADH-quinone oxidoreductase subunit B
46 182 InterPro IPR006138 NADH-ubiquinone oxidoreductase, 20 Kd subunit
43 189 SUPERFAMILY SSF56770 HydA/Nqo6-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 #8
0.79
Show in viewer
Surrounding area
Site 2 FPocket #5
0.543
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.126
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.116
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:133-133
UniProt: Binding site:162-162
UniProt: Binding site:67-67
UniProt: Binding site:68-68
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_A0A0H3GVQ5
AlphaFold DB full sequence Viewing
ColabFold KP13_00992
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.

67 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 17 records from similar proteins
Structural ligands 16 0 loaded crystals
Measured bioactivity 1 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
8Q1 PDB via homolog Detail RCSB PDB
CDL PDB via homolog Detail RCSB PDB
DCQ PDB via homolog Detail RCSB PDB
FES 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 P42026 748.1 Da LogP 12.06 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC…
8Q1 RCSB PDB O75251 540.7 Da LogP 3.29 TPSA 162.3 1 viol. ✓ Clean CCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)…
CDL RCSB PDB Q56218 1464.1 Da LogP 23.31 TPSA 242.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…
DCQ RCSB PDB Q56218 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 A0A1S3U8J5 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
HQH RCSB PDB Q56218 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 Q56218 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 Q56218 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…
PC1 RCSB PDB P42026 790.2 Da LogP 12.17 TPSA 111.2 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])…
PEE RCSB PDB O75251 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 O75251 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 P42026 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 Q56218 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 Q56218 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 P42026 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 P42026 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.