Protein profile

PA4829

dihydrolipoamide dehydrogenase

Genome: NC_002516.2

Gene: PA4829 lpd3 Structure source: AlphaFold UniProt Q9HUY1
Amino acids 467
Annotations 7
Features 36
PDB binders 9
Druggability 0.716

Overview

Basic information about this protein and its source genome.

Accession
PA4829
Gene
PA4829 lpd3
Status
annotated
Amino acids
467
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
66.667
Human E-value
7.729999999999999e-24
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

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.

FPocket 0.716
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0004148 Catalysis of the reaction: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + NAD+ = N(6)-[(R)-lipoyl]-L-lysyl-[protein] + NADH + H+.
  • GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
  • GO:0006103 The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism.
  • 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:0016668 Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces NAD or NADP.

Sequence Features

Domain/signature hits from InterPro and related databases.

36 records
Show feature table
Start End DB Term Name
1 463 PIRSF PIRSF000350 Hg-II_reductase_MerA
1 463 InterPro IPR001100 Pyridine nucleotide-disulphide oxidoreductase, class I
40 50 ProSitePatterns PS00076 Pyridine nucleotide-disulphide oxidoreductases class-I active site.
40 50 InterPro IPR012999 Pyridine nucleotide-disulphide oxidoreductase, class I, active site
6 28 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
409 424 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
431 451 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
39 54 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
344 365 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
141 150 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
267 281 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
177 202 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
309 316 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
347 467 Gene3D G3DSA:3.30.390.30 -
347 467 InterPro IPR016156 FAD/NAD-linked reductase, dimerisation domain superfamily
348 456 Pfam PF02852 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
348 456 InterPro IPR004099 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
347 467 FunFam G3DSA:3.30.390.30:FF:000001 Dihydrolipoyl dehydrogenase
1 375 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
1 375 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
150 273 Gene3D G3DSA:3.50.50.60 -
150 273 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
138 156 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
7 26 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
266 282 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
294 316 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
177 195 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
344 465 SUPERFAMILY SSF55424 FAD/NAD-linked reductases, dimerisation (C-terminal) domain
344 465 InterPro IPR016156 FAD/NAD-linked reductase, dimerisation domain superfamily
6 331 Gene3D G3DSA:3.50.50.60 -
6 331 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
4 465 NCBIfam TIGR01350 dihydrolipoyl dehydrogenase
4 465 InterPro IPR006258 Dihydrolipoamide dehydrogenase
3 459 PANTHER PTHR22912 DISULFIDE OXIDOREDUCTASE
5 329 Pfam PF07992 Pyridine nucleotide-disulphide oxidoreductase
5 329 InterPro IPR023753 FAD/NAD(P)-binding domain

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA4829
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 0.716

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.

69 records

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
3II P9WHH9 625.6 Da LogP 4.65 TPSA 91.4 1 viol. ✓ Clean COc1ccc(c(c1)OC)C(=O)N2CCC3(CC2)C(=O)N(CN3c4ccc…
BTB Q9A0E2 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
GCG P28593 723.9 Da LogP -4.58 TPSA 313.3 3 viol. ✓ Clean C(CCNC(=O)CNC(=O)[C@H](CS)NC(=O)CC[C@@H](C(=O)O…
M52 P9WHH9 429.3 Da LogP 1.69 TPSA 114.6 ✓ Ro5 ✓ Clean C[N@@](CC(=O)Nc1ccc(cc1)OC)S(=O)(=O)c2cc(cnc2N)…
MAE P28593 116.1 Da LogP -0.29 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)/C(=O)O
MLT B4EEF2 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
NHE P09622-2 207.3 Da LogP 0.80 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCS(=O)(=O)O
QUM P28593 468.9 Da LogP 5.83 TPSA 40.6 1 viol. ✓ Clean C[C@@H](CCCN(CCCl)CCCl)/N=C\1/c2ccc(cc2Nc3c1cc(…
RBF Q9A0E2 376.4 Da LogP -1.72 TPSA 161.6 ✓ Ro5 ✓ Clean Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([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.