Protein profile

VK055_0406

diacetyl reductase (S-acetoin forming)

Genome: KpATCC43816

Gene: budC AIK79032.1 Structure source: Experimental + ColabFold UniProt Q48436
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Amino acids 256
Annotations 5
Features 34
PDB binders 6
Druggability 0.457

Overview

Basic information about this protein and its source genome.

Accession
VK055_0406
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
budC AIK79032.1
Status
annotated
Amino acids
256
Structure source
Experimental + ColabFold
EC
1.1.1.304
GO
GO:0045150 The chemical reactions and pathways resulting in the breakdown of acetoin, 3-hydroxy-2-butanone. GO:0019152 Catalysis of the reaction: acetoin + NAD+ = diacetyl + NADH + H+. This reaction is catalyzed in the reverse direction. 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:0052588 Catalysis of the reaction: (S)-acetoin + NAD+ = diacetyl + H+ + NADH. This reaction is catalyzed in the reverse direction.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
41.86
Human E-value
7.64e-11
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
40.784
DEG E-value
3.27e-36
Localization
Cytoplasmic
ColabFold pLDDT
97.24

Selected Druggability evidence

PDB experimental structure

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 0.457
Structure 1GEG
Pocket Pocket 5
P2Rank 0.958
Structure 3WYE
Pocket Pocket 1
ColabFold model
FPocket 0.569 · Pocket 7
P2Rank 0.95 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 152 / 4744 genomes with a hit
Normalized 0.032

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:0045150 The chemical reactions and pathways resulting in the breakdown of acetoin, 3-hydroxy-2-butanone.
  • GO:0019152 Catalysis of the reaction: acetoin + NAD+ = diacetyl + NADH + H+. This reaction is catalyzed in the reverse direction.
  • 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:0052588 Catalysis of the reaction: (S)-acetoin + NAD+ = diacetyl + H+ + NADH. This reaction is catalyzed in the reverse direction.

Sequence Features

Domain/signature hits from InterPro and related databases.

34 records
Show feature table
Start End DB Term Name
20 256 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
78 89 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature
78 89 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
152 171 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature
152 171 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
132 140 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature
132 140 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
1 256 FunFam G3DSA:3.40.50.720:FF:000084 Short-chain dehydrogenase reductase
3 256 NCBIfam TIGR02415 acetoin reductase
3 256 InterPro IPR014007 Acetoin reductase
3 196 Pfam PF00106 short chain dehydrogenase
3 196 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
1 256 CDD cd05366 meso-BDH-like_SDR_c
1 256 Gene3D G3DSA:3.40.50.720 -
139 167 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature.
139 167 InterPro IPR020904 Short-chain dehydrogenase/reductase, conserved site
12 19 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 19 Phobius SIGNAL_PEPTIDE Signal peptide region
173 190 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
173 190 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
4 21 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
4 21 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
126 142 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
126 142 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
78 89 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
152 171 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
217 237 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
217 237 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
3 183 SMART SM00822 This enzymatic domain is part of bacterial polyketide synthases and catalyses the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group.
2 254 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
2 254 InterPro IPR036291 NAD(P)-binding domain superfamily
2 255 PANTHER PTHR24321 DEHYDROGENASES, SHORT CHAIN
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
4 11 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.

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

2 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 3WYE
X-ray 1.58 Å A,B
100.0% 1-256
PDBe RCSB PDBj File
Viewing
PDB 1GEG
X-ray 1.70 Å A,B,C,D,E,F,G,H
100.0% 1-256
PDBe RCSB PDBj File
Loaded
ColabFold VK055_0406
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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 37.52 0.958
2 30.58 0.935
3 0.93 0.004

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.

56 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
A6O
6IHH
C0IR58 314.4 Da LogP 3.93 TPSA 46.5 ✓ Ro5 ✓ Clean CC[C@]1([C@H](CCC1=O)O)C/C=C/2\CCCc3c2ccc(c3)OC
AOI
1NFQ
P9WGT1 290.4 Da LogP 3.96 TPSA 37.3 ✓ Ro5 ✓ Clean C[C@]12CC[C@H](C[C@@H]1CC[C@@H]3[C@@H]2CC[C@]4(…
F3V
6CI9
A0QP46 73.1 Da LogP -0.47 TPSA 43.1 ✓ Ro5 ✓ Clean CC(=O)CN
RM4
7DO7
C1DMX5 164.2 Da LogP -2.19 TPSA 90.2 ✓ Ro5 ✓ Clean C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)O)O)O)O
TAM
4BMN
C0IR58 163.2 Da LogP -1.17 TPSA 86.7 ✓ Ro5 ✓ Clean C(CO)C(CCO)(CCO)N
TLA
5U9P
B4EEX4 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=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.