Protein profile

KP13_01878

Dihydrolipoyl dehydrogenase

Genome: KpKP13

Gene: AHE46318.1 lpdA Structure source: AlphaFold + ColabFold UniProt A0A0H3GJD9
Amino acids 475
Annotations 8
Features 38
PDB binders 14
Druggability 0.981

Overview

Basic information about this protein and its source genome.

Accession
KP13_01878
Gene
AHE46318.1 lpdA
Status
annotated
Amino acids
475
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
52.778
Human E-value
7.04e-16
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
98.105
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 0.895 · Pocket 30
P2Rank 0.968 · 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: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: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:0004148 Catalysis of the reaction: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + NAD+ = N(6)-[(R)-lipoyl]-L-lysyl-[protein] + NADH + H+.
  • 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
178 203 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
9 31 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
266 280 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
309 316 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
142 151 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
344 365 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
42 57 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
5 459 PANTHER PTHR22912 DISULFIDE OXIDOREDUCTASE
347 468 Gene3D G3DSA:3.30.390.30 -
347 468 InterPro IPR016156 FAD/NAD-linked reductase, dimerisation domain superfamily
8 155 FunFam G3DSA:3.50.50.60:FF:000001 Dihydrolipoyl dehydrogenase, mitochondrial
344 467 SUPERFAMILY SSF55424 FAD/NAD-linked reductases, dimerisation (C-terminal) domain
344 467 InterPro IPR016156 FAD/NAD-linked reductase, dimerisation domain superfamily
10 334 Gene3D G3DSA:3.50.50.60 -
10 334 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
1 338 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
1 338 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
151 272 Gene3D G3DSA:3.50.50.60 -
151 272 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
1 470 PIRSF PIRSF000350 Hg-II_reductase_MerA
1 470 InterPro IPR001100 Pyridine nucleotide-disulphide oxidoreductase, class I
43 53 ProSitePatterns PS00076 Pyridine nucleotide-disulphide oxidoreductases class-I active site.
43 53 InterPro IPR012999 Pyridine nucleotide-disulphide oxidoreductase, class I, active site
8 461 NCBIfam TIGR01350 dihydrolipoyl dehydrogenase
8 461 InterPro IPR006258 Dihydrolipoamide dehydrogenase
156 272 FunFam G3DSA:3.50.50.60:FF:000014 Dihydrolipoyl dehydrogenase
347 467 FunFam G3DSA:3.30.390.30:FF:000001 Dihydrolipoyl dehydrogenase
348 456 Pfam PF02852 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
348 456 InterPro IPR004099 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
139 157 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
265 281 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
178 196 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
10 29 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
294 316 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
9 329 Pfam PF07992 Pyridine nucleotide-disulphide oxidoreductase
9 329 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.

3D visualization script Full viewer

Loading 3D structure...

Legend High Medium Low

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 KP13_01878
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.