Protein profile

VK055_0734

dihydrouridine synthase family protein

Genome: KpATCC43816

Gene: AIK79357.1 Structure source: AlphaFold + ColabFold UniProt A0A098CB77
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Amino acids 366
Annotations 5
Features 9
PDB binders 7
Druggability 0.697

Overview

Basic information about this protein and its source genome.

Accession
VK055_0734
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK79357.1
Status
annotated
Amino acids
366
Structure source
AlphaFold + ColabFold
EC
1.6.99.1
GO
GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH. 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:0003959 Catalysis of the reaction: NADPH + H+ + acceptor = NADP+ + reduced acceptor.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
33.043
Localization
Cytoplasmic
ColabFold pLDDT
97.86

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 0.697
Structure A0A098CB77
Pocket Pocket 2
P2Rank 0.889
Structure A0A098CB77
Pocket Pocket 1
ColabFold model
FPocket 0.67 · Pocket 3
P2Rank 0.904 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 89 / 4744 genomes with a hit
Normalized 0.019

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
  • 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:0003959 Catalysis of the reaction: NADPH + H+ + acceptor = NADP+ + reduced acceptor.

Sequence Features

Domain/signature hits from InterPro and related databases.

9 records
Show feature table
Start End DB Term Name
1 354 SUPERFAMILY SSF51395 FMN-linked oxidoreductases
1 363 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 363 InterPro IPR013785 Aldolase-type TIM barrel
2 353 PANTHER PTHR43303 NADPH DEHYDROGENASE C23G7.10C-RELATED
2 353 InterPro IPR044152 NADPH dehydrogenase YqjM-like
4 338 Pfam PF00724 NADH:flavin oxidoreductase / NADH oxidase family
4 338 InterPro IPR001155 NADH:flavin oxidoreductase/NADH oxidase, N-terminal
4 338 CDD cd02932 OYE_YqiM_FMN
4 338 InterPro IPR044152 NADPH dehydrogenase YqjM-like

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_A0A098CB77
AlphaFold — — full sequence — Viewing
ColabFold VK055_0734
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
2 0.697

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 17.96 0.811
2 0.84 0.003

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.

57 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
8CM
4UTJ
Q3ZDM6 162.1 Da LogP 1.50 TPSA 50.4 ✓ Ro5 ✓ Clean c1cc2c(c(c1)O)OC(=O)C=C2
BTB
3GR8
Q5KXG9 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
BU3
3L5L
Q3ZDM6 90.1 Da LogP -0.25 TPSA 40.5 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C)O)O
COU
3L5M
Q3ZDM6 146.1 Da LogP 1.79 TPSA 30.2 ✓ Ro5 ✓ Clean c1ccc2c(c1)C=CC(=O)O2
FNR
3N19
Q3ZDM6 458.4 Da LogP -0.93 TPSA 208.4 1 viol. ✓ Clean Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C…
HBA
3HGJ
B0JDW3 122.1 Da LogP 1.20 TPSA 37.3 ✓ Ro5 ✓ Clean c1cc(ccc1C=O)O
MLI
7O0T
B8G5D6 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=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.