Overview
Basic information about this protein and its source genome.
- Accession
- PA4538
- Gene
- PA4538 ndh
- Status
- annotated
- Amino acids
- 435
- Structure source
- AlphaFold
Target profile
Computed evidence for target prioritization.
- Human off-target
- No hit
- Gut microbiome off-target
- hit
- Essential (DEG)
- N
- Localization
- CytoplasmicMembrane
Selected Druggability evidence
Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Gene Ontology (GO)
2- GO:0008137 Catalysis of the reaction: NADH + ubiquinone + 5 H+(in) = NAD+ + ubiquinol + 4 H+(out).
- 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.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 3 | 403 | PANTHER | PTHR42913 | APOPTOSIS-INDUCING FACTOR 1 |
| 2 | 319 | SUPERFAMILY | SSF51905 | FAD/NAD(P)-binding domain |
| 2 | 319 | InterPro | IPR036188 | FAD/NAD(P)-binding domain superfamily |
| 5 | 24 | PRINTS | PR00368 | FAD-dependent pyridine nucleotide reductase signature |
| 170 | 188 | PRINTS | PR00368 | FAD-dependent pyridine nucleotide reductase signature |
| 293 | 315 | PRINTS | PR00368 | FAD-dependent pyridine nucleotide reductase signature |
| 112 | 130 | PRINTS | PR00368 | FAD-dependent pyridine nucleotide reductase signature |
| 2 | 415 | Gene3D | G3DSA:3.50.50.100 | - |
| 2 | 415 | FunFam | G3DSA:3.50.50.100:FF:000001 | NADH dehydrogenase |
| 4 | 341 | Pfam | PF07992 | Pyridine nucleotide-disulphide oxidoreductase |
| 4 | 341 | InterPro | IPR023753 | FAD/NAD(P)-binding domain |
| 308 | 315 | PRINTS | PR00411 | Pyridine nucleotide disulphide reductase class-I signature |
| 170 | 195 | PRINTS | PR00411 | Pyridine nucleotide disulphide reductase class-I signature |
| 4 | 26 | PRINTS | PR00411 | Pyridine nucleotide disulphide reductase class-I signature |
3D Structure
Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.
Loading 3D structure...
Structural evidence
0 + 1Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
PA4538
|
AlphaFold | — | — | full sequence | — | Viewing |
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer
Pockets (FPOCKET)
Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).
| FPOCKET | Sticks | Spheres | Surfaces | Druggability | Labels | Zoom | Positions |
|---|---|---|---|---|---|---|---|
| 1 | 0.824 |
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.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| 8WF | P32340 | 329.5 Da LogP 5.64 TPSA 47.2 | 1 viol. | Alert |
CCCCCCCCCCCCc1cc(c2ccccc2[n+]1[O-])O
|
|
| HQO | F5L3B8 | 259.3 Da LogP 3.69 TPSA 47.2 | ✓ Ro5 | Alert |
CCCCCCCc1cc(c2ccccc2[n+]1[O-])O
|
|
| MLI | Q2FZV7 | 102.0 Da LogP -3.12 TPSA 80.3 | ✓ Ro5 | ✓ Clean |
C(C(=O)[O-])C(=O)[O-]
|
|
| MYX | P32340 | 487.7 Da LogP 5.82 TPSA 87.3 | 1 viol. | ✓ Clean |
C[C@@H](/C=C/C=C/C(C)C)c1nc(cs1)c2nc(cs2)/C=C/[…
|
|
| PE4 | P32340 | 354.4 Da LogP 0.11 TPSA 84.8 | ✓ Ro5 | ✓ Clean |
CCOCCOCCOCCOCCOCCOCCOCCO
|
|
| SMA | P32340 | 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…
|
|
| TRT | P32340 | 352.5 Da LogP 4.46 TPSA 36.9 | ✓ Ro5 | ✓ Clean |
CC(C)(C)CC(C)(C)c1ccc(cc1)OCCOCCOCCOC
|
|
| UQ2 | P32340 | 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
|
|
| UQ5 | P32340 | 522.8 Da LogP 9.22 TPSA 52.6 | 2 viol. | Alert |
CC1=C(C(=O)C(=C(C1=O)OC)OC)C\C=C(/C)\CC\C=C(/C)…
|
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
| Ligand | UniProt (homolog) | pchembl | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| CHEMBL5202255 | P95160 | 7.50 | 397.4 Da LogP 3.30 TPSA 45.7 | ✓ Ro5 | ✓ Clean |
CC(C)[C@H]1CO[C@]23CCN(Cc4ccc(C(F)(F)F)nc4)C[C@…
|
| CHEMBL5186518 | P95200 | 7.24 | 412.5 Da LogP 3.78 TPSA 42.0 | ✓ Ro5 | ✓ Clean |
CC(C)[C@H]1CO[C@]23CCN(Cc4ccc(OC(F)(F)F)cc4)C[C…
|
| CHEMBL5201484 | P95200 | 7.23 | 396.5 Da LogP 3.90 TPSA 32.8 | ✓ Ro5 | ✓ Clean |
CC(C)[C@H]1CO[C@]23CCN(Cc4ccc(C(F)(F)F)cc4)C[C@…
|
| CHEMBL5171834 | P95200 | 7.02 | 362.9 Da LogP 3.54 TPSA 32.8 | ✓ Ro5 | ✓ Clean |
CC(C)[C@H]1CO[C@]23CCN(Cc4ccc(Cl)cc4)C[C@H]2CCC…
|
| CHEMBL5206556 | P95160 | 6.70 | 358.5 Da LogP 2.89 TPSA 42.0 | ✓ Ro5 | ✓ Clean |
COc1ccc(CN2CC[C@]34OC[C@H](C(C)C)N3C(=O)CC[C@@H…
|
| CHEMBL5182198 | P95200 | 6.01 | 328.5 Da LogP 2.88 TPSA 32.8 | ✓ Ro5 | ✓ Clean |
CC(C)[C@H]1CO[C@]23CCN(Cc4ccccc4)C[C@H]2CCC(=O)…
|
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC12501520 | 1.000 | 458.5 Da LogP -0.88 TPSA 123.5 | 1 viol. | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC1529909 | 1.000 | 259.3 Da LogP 3.69 TPSA 47.2 | ✓ Ro5 | Alert |
CCCCCCCc1cc(O)c2ccccc2[n+]1[O-]
|
| ZINC1532641 | 1.000 | 318.4 Da LogP 4.04 TPSA 52.6 | ✓ Ro5 | Alert |
COC1=C(OC)C(=O)C(C/C=C(\C)CCC=C(C)C)=C(C)C1=O
|
| ZINC3874716 | 1.000 | 414.5 Da LogP -0.90 TPSA 114.3 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC4283769 | 1.000 | 238.3 Da LogP -0.96 TPSA 77.4 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCO
|
| ZINC4521548 | 1.000 | 282.3 Da LogP -0.95 TPSA 86.6 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCO
|
| ZINC5178829 | 1.000 | 326.4 Da LogP -0.93 TPSA 95.8 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCO
|
| ZINC5178830 | 1.000 | 370.4 Da LogP -0.91 TPSA 105.1 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC5650743 | 1.000 | 222.3 Da LogP 0.07 TPSA 57.2 | ✓ Ro5 | ✓ Clean |
CCOCCOCCOCCOCCO
|
| ZINC6403917 | 1.000 | 354.4 Da LogP 0.11 TPSA 84.8 | ✓ Ro5 | ✓ Clean |
CCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC1559692 | 0.750 | 250.3 Da LogP 2.32 TPSA 52.6 | ✓ Ro5 | Alert |
COC1=C(OC)C(=O)C(CC=C(C)C)=C(C)C1=O
|
| ZINC2030966 | 0.750 | 294.4 Da LogP 3.79 TPSA 38.7 | ✓ Ro5 | ✓ Clean |
CC(C)(C)CC(C)(C)c1ccc(OCCOCCO)cc1
|
| ZINC1592053 | 0.711 | 321.5 Da LogP 4.36 TPSA 21.7 | ✓ Ro5 | ✓ Clean |
CN(C)CCOCCOc1ccc(C(C)(C)CC(C)(C)C)cc1
|
| ZINC167273021 | 0.692 | 308.4 Da LogP 3.88 TPSA 55.8 | ✓ Ro5 | ✓ Clean |
CC(C)(C)CC(C)(C)c1ccc(OCCOCC(=O)O)cc1
|
| ZINC115086873 | 0.688 | 209.2 Da LogP -1.08 TPSA 83.2 | ✓ Ro5 | ✓ Clean |
NOCCOCCOCCOCCO
|
| ZINC137432264 | 0.688 | 457.6 Da LogP -0.91 TPSA 129.3 | 1 viol. | ✓ Clean |
NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC146143823 | 0.688 | 237.3 Da LogP -1.00 TPSA 83.2 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCO
|
| ZINC1542984442 | 0.688 | 413.5 Da LogP -0.93 TPSA 120.1 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC1565503710 | 0.688 | 254.3 Da LogP -0.03 TPSA 57.2 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCS
|
| ZINC1580161 | 0.688 | 208.3 Da LogP -0.33 TPSA 57.2 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCO
|
| ZINC16052118 | 0.688 | 340.4 Da LogP -0.28 TPSA 84.8 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCO
|
| ZINC16052257 | 0.688 | 384.5 Da LogP -0.26 TPSA 94.1 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC1857792028 | 0.688 | 430.6 Da LogP 0.04 TPSA 94.1 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCOCCS
|
| ZINC1857792057 | 0.688 | 474.6 Da LogP 0.06 TPSA 103.3 | 1 viol. | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS
|
| ZINC230494776 | 0.688 | 325.4 Da LogP -0.96 TPSA 101.6 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCOCCOCCO
|
| ZINC34317654 | 0.688 | 472.6 Da LogP -0.23 TPSA 112.5 | 1 viol. | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC38917157 | 0.688 | 210.3 Da LogP -0.04 TPSA 47.9 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCS
|
| ZINC44076059 | 0.688 | 428.5 Da LogP -0.24 TPSA 103.3 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC5210101 | 0.688 | 252.3 Da LogP -0.31 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCO
|
| ZINC5859031 | 0.688 | 294.4 Da LogP 1.13 TPSA 55.4 | ✓ Ro5 | ✓ Clean |
CCOCCOCCOCCOCCOCCOCC
|
| ZINC5997860 | 0.688 | 296.4 Da LogP -0.29 TPSA 75.6 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCO
|
| ZINC77271182 | 0.688 | 281.3 Da LogP -0.98 TPSA 92.4 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCOCCO
|
| ZINC83253921 | 0.688 | 369.5 Da LogP -0.95 TPSA 110.9 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCOCCOCCOCCO
|
| ZINC90741446 | 0.688 | 386.5 Da LogP 0.02 TPSA 84.8 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCOCCOCCS
|
| ZINC90741447 | 0.688 | 298.4 Da LogP -0.01 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCCOCCS
|
| ZINC144169243 | 0.647 | 281.3 Da LogP -1.37 TPSA 89.4 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCNCCOCCOCCO
|
| ZINC205758716 | 0.647 | 457.6 Da LogP -1.31 TPSA 126.3 | 1 viol. | ✓ Clean |
OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO
|
| ZINC575441396 | 0.647 | 369.5 Da LogP -1.34 TPSA 107.9 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCNCCOCCOCCOCCO
|
| ZINC25756964 | 0.645 | 402.5 Da LogP 1.80 TPSA 73.8 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOc1ccc(OCCOCCOCCOC)cc1
|
| ZINC1532311 | 0.639 | 250.4 Da LogP 3.77 TPSA 29.5 | ✓ Ro5 | ✓ Clean |
CC(C)(C)CC(C)(C)c1ccc(OCCO)cc1
|
| ZINC1857731210 | 0.631 | 368.4 Da LogP 3.26 TPSA 32.8 | ✓ Ro5 | ✓ Clean |
CC(C)[C@@H]1CO[C@@]23CCN(Cc4ccc(C(F)(F)F)cc4)[C…
|
| ZINC4353076 | 0.628 | 352.5 Da LogP 4.42 TPSA 68.3 | ✓ Ro5 | ✓ Clean |
CC(C)(C)CC(C)(C)c1ccc(OCCOCCSC(=N)N)cc1
|
| ZINC1688152 | 0.622 | 380.5 Da LogP 3.96 TPSA 55.8 | ✓ Ro5 | ✓ Clean |
CC(C)(C)CC(C)(C)c1ccc(OCCOCC[N+](C)(C)CC(=O)O)c…
|
| ZINC1644613 | 0.619 | 206.3 Da LogP 0.83 TPSA 47.9 | ✓ Ro5 | ✓ Clean |
CCCCOCCOCCOCCO
|
| ZINC258839852 | 0.611 | 276.3 Da LogP 0.61 TPSA 57.2 | ✓ Ro5 | ✓ Clean |
OCCOCCOCCOCCOCC(F)(F)F
|
| ZINC35650209 | 0.605 | 278.4 Da LogP 4.55 TPSA 29.5 | ✓ Ro5 | ✓ Clean |
CC(C)(C)CC(C)(C)c1ccc(OCCCCO)cc1
|
| ZINC226069334 | 0.605 | 366.6 Da LogP 3.86 TPSA 38.7 | ✓ Ro5 | ✓ Clean |
CC(C)(C)CC(C)(C)c1ccc(OCCOC[C@@H](O)C[N+](C)(C)…
|
| ZINC226069348 | 0.605 | 366.6 Da LogP 3.86 TPSA 38.7 | ✓ Ro5 | ✓ Clean |
CC(C)(C)CC(C)(C)c1ccc(OCCOC[C@H](O)C[N+](C)(C)C…
|
| ZINC32011214 | 0.600 | 363.5 Da LogP 4.13 TPSA 30.9 | ✓ Ro5 | ✓ Clean |
CC(C)(C)CC(C)(C)c1ccc(OCCOCCN2CCOCC2)cc1
|
| ZINC34160867 | 0.600 | 222.3 Da LogP -0.20 TPSA 68.2 | ✓ Ro5 | ✓ Clean |
OCCCOCCOCCOCCCO
|
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.