Protein profile

VK055_2450

dihydrolipoyl dehydrogenase

Genome: KpATCC43816

Gene: AIK81047.1 lpdA2 Structure source: AlphaFold + ColabFold UniProt A0A0H3GJD9
Amino acids 474
Annotations 8
Features 38
PDB binders 14
Druggability 0.981

Overview

Basic information about this protein and its source genome.

Accession
VK055_2450
Gene
AIK81047.1 lpdA2
Status
annotated
Amino acids
474
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
52.778
Human E-value
7.09e-16
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
98.312
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.1

Selected Druggability evidence

AlphaFold / UniProt model

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 0.981
Structure A0A0H3GJD9
Pocket Pocket 33
P2Rank 0.953
Structure A0A0H3GJD9
Pocket Pocket 1
ColabFold model
FPocket 0.923 · Pocket 28
P2Rank 0.982 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 172 / 4744 genomes with a hit
Normalized 0.036

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0004148 Catalysis of the reaction: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + NAD+ = N(6)-[(R)-lipoyl]-L-lysyl-[protein] + NADH + H+.
  • 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.
  • 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: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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • 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:0006979 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.

Sequence Features

Domain/signature hits from InterPro and related databases.

38 records
Show feature table
Start End DB Term Name
347 455 Pfam PF02852 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
347 455 InterPro IPR004099 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
4 458 PANTHER PTHR22912 DISULFIDE OXIDOREDUCTASE
346 467 Gene3D G3DSA:3.30.390.30 -
346 467 InterPro IPR016156 FAD/NAD-linked reductase, dimerisation domain superfamily
7 460 NCBIfam TIGR01350 dihydrolipoyl dehydrogenase
7 460 InterPro IPR006258 Dihydrolipoamide dehydrogenase
343 466 SUPERFAMILY SSF55424 FAD/NAD-linked reductases, dimerisation (C-terminal) domain
343 466 InterPro IPR016156 FAD/NAD-linked reductase, dimerisation domain superfamily
1 469 PIRSF PIRSF000350 Hg-II_reductase_MerA
1 469 InterPro IPR001100 Pyridine nucleotide-disulphide oxidoreductase, class I
7 154 FunFam G3DSA:3.50.50.60:FF:000001 Dihydrolipoyl dehydrogenase, mitochondrial
346 466 FunFam G3DSA:3.30.390.30:FF:000001 Dihydrolipoyl dehydrogenase
150 271 Gene3D G3DSA:3.50.50.60 -
150 271 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
408 423 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
141 150 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
430 450 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
177 202 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
343 364 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
41 56 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
265 279 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
308 315 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
8 30 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
2 337 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
2 337 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
9 333 Gene3D G3DSA:3.50.50.60 -
9 333 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
264 280 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
293 315 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
9 28 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
138 156 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
177 195 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
155 271 FunFam G3DSA:3.50.50.60:FF:000014 Dihydrolipoyl dehydrogenase
8 328 Pfam PF07992 Pyridine nucleotide-disulphide oxidoreductase
8 328 InterPro IPR023753 FAD/NAD(P)-binding domain
42 52 ProSitePatterns PS00076 Pyridine nucleotide-disulphide oxidoreductases class-I active site.
42 52 InterPro IPR012999 Pyridine nucleotide-disulphide oxidoreductase, class I, active site

3D Structure

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

3D visualization script Full viewer

Loading 3D structure...

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Structural evidence

0 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GJD9
AlphaFold full sequence Viewing
ColabFold VK055_2450
ColabFold full sequence Loaded
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
33 0.981

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 25.27 0.905
2 3.38 0.121
3 3.27 0.114
4 2.11 0.048
5 2.07 0.046

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.

71 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…
ACM P00390 59.1 Da LogP -0.51 TPSA 43.1 ✓ Ro5 ✓ Clean CC(=O)N
AUP P00390 368.4 Da LogP 6.67 TPSA 25.8 1 viol. ✓ Clean c1ccc(cc1)p2c(c3c(c2c4ccccn4)CCCC3)c5ccccn5
BTB P09622-2 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
ELI P00390 286.3 Da LogP 3.42 TPSA 71.4 ✓ Ro5 Alert CC1=C(C(=O)c2ccccc2C1=O)CCCCCC(=O)O
GCG P00390 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…
GDS P00390 612.6 Da LogP -3.88 TPSA 317.6 3 viol. ✓ Clean C(CC(=O)N[C@@H](CSSC[C@@H](C(=O)NCC(=O)O)NC(=O)…
GSH P00390 307.3 Da LogP -2.21 TPSA 158.8 1 viol. ✓ Clean C(CC(=O)N[C@@H](CS)C(=O)NCC(=O)O)[C@@H](C(=O)O)N
HXP P00390 286.3 Da LogP 3.20 TPSA 87.0 ✓ Ro5 ✓ Clean c1cc2c(cc1O)Oc3cc(ccc3C2CCC(=O)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
RGS P00390 612.6 Da LogP -3.88 TPSA 317.6 3 viol. ✓ Clean C(CNC(=O)[C@@H](CSSC[C@H](C(=O)NCC[C@@H](C(=O)O…
TS2 P00390 721.9 Da LogP -4.04 TPSA 313.3 3 viol. ✓ Clean C1CCNC(=O)CNC(=O)[C@H](CSSC[C@@H](C(=O)NCC(=O)N…
TS4 P00390 867.1 Da LogP -4.38 TPSA 377.3 3 viol. ✓ Clean C(CCNCCCNC(=O)CNC(=O)[C@H](CSSC[C@@H](C(=O)NCC(…

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.