Protein target profile

KP13_00982

NADH-quinone oxidoreductase subunit M

Genome: KpKP13 Gene: nuoM AHE43488.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GVP8
Length 509
Pocket druggability 0.926
Direct ligand evidence 0 73 total records
Functional annotation 0 EC 7 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 (%)
32.425 Lower values reduce human off-target concern.
Human E-value
2.840000000000001e-44
Gut microbiome similarity
2.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
61.522 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
94.68 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 0.926
Structure A0A0H3GVP8
Pocket Pocket 6
P2Rank 0.535
Structure A0A0H3GVP8
Pocket Pocket 1
ColabFold model
FPocket 0.88 · Pocket 2
P2Rank 0.536 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 135 / 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.

MLLPWLILIPFIGGFLCWQTERFGVKVPRWIALITMGLTLVLGLQLWMQGGYSLTQSAGIPQWQSEFVLPWIPRFGISIHLAIDGLSLLMVVLTGLLGVLAVLCSWREIEKYQGFFHLNLMWILGGVIGVFLAIDMFLFFFFWEMMLVPMYFLIALWGHKASDGKTRITAATKFFIYTQASGLVMLIAILALAFVHFNATGVWTFNYEELLKTPMSHGVEYLLMLGFFIAFAVKMPVVPLHGWLPDAHSQAPTAGSVDLAGILLKTAAYGLLRFALPLFPNASAEFAPIAMWLGVIGIFYGAWMAFAQTDIKRLIAYTSVSHMGFVLIAIYTGSQLAYQGAVIQMIAHGLSAAGLFILCGQLYERLHTRDMRQMGGLWSKIKWLPAMSMFFAVATLGMPGTGNFVGEFMILFGSYKVVPTITVISTFGLVFASVYSLSMLHRAYFGKAKSEVAAKELPGMSLRELSIILLLVVLLVLLGFFPQPILDTSHAAMSNIQQWFVNSVSTTRP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • GO:0042773 The transfer of electrons through a series of electron donors and acceptors, generating energy that is ultimately used for synthesis of ATP.
  • GO:0008137 Catalysis of the reaction: NADH + ubiquinone + 5 H+(in) = NAD+ + ubiquinol + 4 H+(out).
  • GO:0012505 A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0003954 Catalysis of the reaction: NADH + H+ + acceptor = NAD+ + reduced acceptor.
  • GO:0048039 Binding to ubiquinone, a quinone derivative with a tail of isoprene units.
  • 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.

59 records
Show feature table
Start End DB Term Name
49 76 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
4 18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
245 255 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
24 29 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
160 179 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
104 114 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
30 49 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
341 363 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
221 244 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
314 333 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
77 103 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
135 139 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
314 336 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
202 220 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
289 307 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
140 159 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
115 134 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
337 356 PRINTS PR01437 NADH-ubiquinone oxidoreductase subunit 4 signature
337 356 InterPro IPR003918 NADH:ubiquinone oxidoreductase
249 273 PRINTS PR01437 NADH-ubiquinone oxidoreductase subunit 4 signature
249 273 InterPro IPR003918 NADH:ubiquinone oxidoreductase
389 415 PRINTS PR01437 NADH-ubiquinone oxidoreductase subunit 4 signature
389 415 InterPro IPR003918 NADH:ubiquinone oxidoreductase
139 158 PRINTS PR01437 NADH-ubiquinone oxidoreductase subunit 4 signature
139 158 InterPro IPR003918 NADH:ubiquinone oxidoreductase
174 198 PRINTS PR01437 NADH-ubiquinone oxidoreductase subunit 4 signature
174 198 InterPro IPR003918 NADH:ubiquinone oxidoreductase
174 196 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
441 460 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
115 134 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
383 402 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
222 244 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
288 307 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
81 103 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
30 48 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
180 201 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
3 499 NCBIfam TIGR01972 NADH-quinone oxidoreductase subunit M
3 499 InterPro IPR010227 NADH-quinone oxidoreductase, chain M/4
334 344 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
364 382 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
257 279 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
464 486 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
461 481 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
308 313 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
345 363 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 497 PANTHER PTHR43507 NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 4
1 497 InterPro IPR003918 NADH:ubiquinone oxidoreductase
6 23 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
277 287 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
417 439 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
406 416 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
256 276 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
139 161 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
383 405 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
134 430 Pfam PF00361 Proton-conducting membrane transporter
134 430 InterPro IPR001750 NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit
482 509 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
417 440 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.

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 · FPocket

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

Site 1 FPocket #6
0.926
Likely same site as P2Rank 1 1.6 Å 15 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #11
0.481
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.535
Likely same site as FPocket 6 1.6 Å 15 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.273
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.089
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.061
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.059
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_A0A0H3GVP8
AlphaFold DB full sequence Viewing
ColabFold KP13_00982
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.

73 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 23 records from similar proteins
Structural ligands 23 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
BCR PDB via homolog Detail RCSB PDB
CDL PDB via homolog Detail RCSB PDB
CPL PDB via homolog Detail RCSB PDB
DGD 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 P03910 748.1 Da LogP 12.06 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC…
BCR RCSB PDB Q8DKY0 536.9 Da LogP 12.61 TPSA 0.0 2 viol. ✓ Clean CC1=C(C(CCC1)(C)C)\C=C\C(=C\C=C\C(=C\C=C\C=C(/C…
CDL RCSB PDB Q9B6D6 1464.1 Da LogP 23.31 TPSA 242.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…
CPL RCSB PDB Q9B6D6 758.1 Da LogP 10.94 TPSA 111.2 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])OC…
DGD RCSB PDB Q8DKY0 949.3 Da LogP 7.61 TPSA 231.1 4 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[C@H]1[C@@H]([C…
EHZ RCSB PDB Q9B6D6 584.7 Da LogP 3.04 TPSA 182.5 2 viol. ✓ Clean CCCCCCCCCCC[C@@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H]…
FES RCSB PDB Q9B6D6 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
LHG RCSB PDB Q8DKY0 723.0 Da LogP 9.89 TPSA 148.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@…
LMG RCSB PDB Q8DKY0 787.2 Da LogP 9.78 TPSA 152.0 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[C@H]1[C@@H]([C…
LMN RCSB PDB Q9B6D6 1005.2 Da LogP -1.68 TPSA 357.1 3 viol. ✓ Clean CCCCCCCCCCC(CCCCCCCCCC)(CO[C@@H]1[C@@H]([C@@H](…
LMT RCSB PDB Q9B6D6 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…
PC1 RCSB PDB P03910 790.2 Da LogP 12.17 TPSA 111.2 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])…
PGT RCSB PDB Q8DKF4 751.0 Da LogP 10.67 TPSA 148.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)O[C@@H](COC(=O)CCCCCCCCCC…
PL9 RCSB PDB Q8DKY0 749.2 Da LogP 16.57 TPSA 34.1 2 viol. Alert CC1=C(C(=O)C(=CC1=O)CC=C(C)CCC=C(C)CCC=C(C)CCC=…
PLC RCSB PDB Q9B6D6 622.8 Da LogP 8.12 TPSA 108.4 2 viol. ✓ Clean CCCCCCCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)…
PQN RCSB PDB Q8DKY0 450.7 Da LogP 9.16 TPSA 34.1 1 viol. Alert CC1=C(C(=O)c2ccccc2C1=O)C\C=C(/C)\CCC[C@H](C)CC…
PSC RCSB PDB Q9B6D6 759.1 Da LogP 11.58 TPSA 108.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCC[N…
SQD RCSB PDB Q8DKY0 795.1 Da LogP 8.12 TPSA 186.1 3 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](COC1[C@@H]([C@H]([C…
T7X RCSB PDB Q9B6D6 887.1 Da LogP 9.17 TPSA 209.5 4 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OC1[C@@…
UMQ RCSB PDB Q56228 496.6 Da LogP -0.84 TPSA 178.5 2 viol. ✓ Clean CCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)…
UQ2 RCSB PDB P03910 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
UQ9 RCSB PDB Q9B6D6 795.2 Da LogP 16.13 TPSA 52.6 2 viol. Alert CC1=C(C(=O)C(=C(C1=O)OC)OC)C\C=C(/C)\CC\C=C(/C)…
ZMP RCSB PDB Q9B6D6 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.