Protein profile

VK055_3958

NADH:flavin oxidoreductase / NADH oxidase familyprotein

Genome: KpATCC43816

Gene: AIK82506.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GYQ7
Export view
Amino acids 673
Annotations 6
Features 22
PDB binders 4
Druggability 0.714

Overview

Basic information about this protein and its source genome.

Accession
VK055_3958
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82506.1
Status
annotated
Amino acids
673
Structure source
AlphaFold + ColabFold
GO
GO:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes. 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:0008670 Catalysis of the reactions: a 4,5-saturated-(2E)-enoyl-CoA + NADP+ = a (2E,4E)-dienoyl-CoA + H+ + NADPH, and a (2E,4Z)-dienoyl-CoA + H+ + NADPH = a 4,5-saturated-(2E)-enoyl-CoA + NADP+. GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms. GO:0046872 Binding to a metal ion. GO:0033543 A fatty acid beta-oxidation pathway by which fatty acids having cis-double bonds on even-numbered carbons are degraded. In this pathway, the intermediate 2,4-dienoyl-CoA is converted to trans-2-enoyl-CoA by 2,4-dienoyl-CoA reductase and delta3-delta2-enoyl-CoA isomerase; trans-2-enoyl-CoA returns to the core beta-oxidation pathway for further degradation. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
83.582
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.64

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 0.714
Structure A0A0H3GYQ7
Pocket Pocket 30
P2Rank 0.987
Structure A0A0H3GYQ7
Pocket Pocket 1
ColabFold model
FPocket 0.644 · Pocket 31
P2Rank 0.966 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 159 / 4744 genomes with a hit
Normalized 0.034

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
  • 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:0008670 Catalysis of the reactions: a 4,5-saturated-(2E)-enoyl-CoA + NADP+ = a (2E,4E)-dienoyl-CoA + H+ + NADPH, and a (2E,4Z)-dienoyl-CoA + H+ + NADPH = a 4,5-saturated-(2E)-enoyl-CoA + NADP+.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0046872 Binding to a metal ion.
  • GO:0033543 A fatty acid beta-oxidation pathway by which fatty acids having cis-double bonds on even-numbered carbons are degraded. In this pathway, the intermediate 2,4-dienoyl-CoA is converted to trans-2-enoyl-CoA by 2,4-dienoyl-CoA reductase and delta3-delta2-enoyl-CoA isomerase; trans-2-enoyl-CoA returns to the core beta-oxidation pathway for further degradation. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
3 369 Gene3D G3DSA:3.20.20.70 Aldolase class I
3 369 InterPro IPR013785 Aldolase-type TIM barrel
6 332 Pfam PF00724 NADH:flavin oxidoreductase / NADH oxidase family
6 332 InterPro IPR001155 NADH:flavin oxidoreductase/NADH oxidase, N-terminal
498 516 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
619 635 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
378 397 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
377 399 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
620 634 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
3 363 SUPERFAMILY SSF51395 FMN-linked oxidoreductases
377 653 Pfam PF07992 Pyridine nucleotide-disulphide oxidoreductase
377 653 InterPro IPR023753 FAD/NAD(P)-binding domain
1 673 PANTHER PTHR42917 2,4-DIENOYL-COA REDUCTASE
7 359 CDD cd02930 DCR_FMN
470 626 FunFam G3DSA:3.50.50.60:FF:000113 NADPH-dependent 2,4-dienoyl-CoA reductase
462 651 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
462 651 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
470 626 Gene3D G3DSA:3.50.50.60 -
470 626 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
376 666 Gene3D G3DSA:3.40.50.720 -
3 370 FunFam G3DSA:3.20.20.70:FF:000082 NADPH-dependent 2,4-dienoyl-CoA reductase
334 520 SUPERFAMILY SSF51971 Nucleotide-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_A0A0H3GYQ7
AlphaFold — — full sequence — Viewing
ColabFold VK055_3958
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
30 0.714
17 0.372
1 0.341

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 30.66 0.935
2 21.36 0.869
3 13.11 0.674
4 10.88 0.584
5 5.54 0.265

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.

54 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
HBA
1Z42
P54550 122.1 Da LogP 1.20 TPSA 37.3 ✓ Ro5 ✓ Clean c1cc(ccc1C=O)O
J5H
6QKR
E1YD54 921.7 Da LogP 1.13 TPSA 363.6 3 viol. ✓ Clean CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([…
MDE
1PS9
P42593 994.9 Da LogP 0.91 TPSA 382.6 3 viol. ✓ Clean CCCCC[C@@H](C\C=C\C(=O)SCCNC(=O)CCNC(C(=O)C(C)(…
NPO
1Z44
P54550 139.1 Da LogP 1.30 TPSA 63.4 ✓ Ro5 ✓ Clean c1cc(ccc1[N+](=O)[O-])O

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.