Protein profile

VK055_0533

benzyl alcohol dehydrogenase

Genome: KpATCC43816

Gene: AIK79156.1 xylB Structure source: AlphaFold + ColabFold UniProt A0A0H3GU94
Export view
Amino acids 360
Annotations 5
Features 19
PDB binders 9
Druggability 0.894

Overview

Basic information about this protein and its source genome.

Accession
VK055_0533
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK79156.1 xylB
Status
annotated
Amino acids
360
Structure source
AlphaFold + ColabFold
GO
GO:0008270 Binding to a zinc ion (Zn). 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0051903 Catalysis of the reaction: S-(hydroxymethyl)glutathione + NAD(P)+ = S-formylglutathione + NAD(P)H + H+. GO:0046294 The chemical reactions and pathways resulting in the breakdown of formaldehyde (methanal, H2C=O), the simplest aldehyde.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
51.282
Human E-value
1.07e-15
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
32.24
Localization
Cytoplasmic
ColabFold pLDDT
97.35

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 0.894
Structure A0A0H3GU94
Pocket Pocket 16
P2Rank 0.951
Structure A0A0H3GU94
Pocket Pocket 1
ColabFold model
FPocket 0.874 · Pocket 5
P2Rank 0.955 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 35 / 4744 genomes with a hit
Normalized 0.007

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0008270 Binding to a zinc ion (Zn).
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0051903 Catalysis of the reaction: S-(hydroxymethyl)glutathione + NAD(P)+ = S-formylglutathione + NAD(P)H + H+.
  • GO:0046294 The chemical reactions and pathways resulting in the breakdown of formaldehyde (methanal, H2C=O), the simplest aldehyde.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
170 304 Gene3D G3DSA:3.40.50.720 -
58 72 ProSitePatterns PS00059 Zinc-containing alcohol dehydrogenases signature.
58 72 InterPro IPR002328 Alcohol dehydrogenase, zinc-type, conserved site
8 359 SMART SM00829 PKS_ER_names_mod
8 359 InterPro IPR020843 Polyketide synthase, enoylreductase domain
8 351 Gene3D G3DSA:3.90.180.10 -
170 304 FunFam G3DSA:3.40.50.720:FF:000003 S-(hydroxymethyl)glutathione dehydrogenase
26 115 Pfam PF08240 Alcohol dehydrogenase GroES-like domain
26 115 InterPro IPR013154 Alcohol dehydrogenase-like, N-terminal
314 359 SUPERFAMILY SSF50129 GroES-like
314 359 InterPro IPR011032 GroES-like superfamily
2 352 PANTHER PTHR43880 ALCOHOL DEHYDROGENASE
156 326 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
156 326 InterPro IPR036291 NAD(P)-binding domain superfamily
1 189 SUPERFAMILY SSF50129 GroES-like
1 189 InterPro IPR011032 GroES-like superfamily
193 308 Pfam PF00107 Zinc-binding dehydrogenase
193 308 InterPro IPR013149 Alcohol dehydrogenase-like, C-terminal
2 359 CDD cd08278 benzyl_alcohol_DH

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_A0A0H3GU94
AlphaFold — — full sequence — Viewing
ColabFold VK055_0533
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
16 0.894

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 25.61 0.908
2 1.58 0.025
3 0.75 0.002

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.

78 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
022
3QJ5
P11766 414.5 Da LogP 3.75 TPSA 103.1 ✓ Ro5 Alert Cc1cc(ccc1n2c(ccc2c3ccc(cc3)n4ccnc4)CCC(=O)O)C(…
12H
1M6W
P11766 216.3 Da LogP 2.96 TPSA 57.5 ✓ Ro5 ✓ Clean C(CCCCCC(=O)O)CCCCCO
AHE
1MC5
P11766 337.4 Da LogP -2.45 TPSA 179.1 1 viol. ✓ Clean C(CC(=O)N[C@@H](CSCO)C(=O)NCC(=O)O)[C@@H](C(=O)…
APR
2FZE
P11766 559.3 Da LogP -3.28 TPSA 291.5 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
CXL
1HDX
P00325 100.2 Da LogP 1.31 TPSA 20.2 ✓ Ro5 ✓ Clean C1CCC(CC1)O
DAO
1MA0
P11766 200.3 Da LogP 3.99 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCCCC(=O)O
FXY
1U3W
P00326 157.3 Da LogP 2.09 TPSA 29.1 ✓ Ro5 ✓ Clean CCCCCC[C@@H](C)NC=O
N2P
3QJ5
P11766 102.2 Da LogP 0.07 TPSA 52.0 ✓ Ro5 ✓ Clean C(CCN)CCN
PYZ
1HSO
P07327 194.0 Da LogP 1.01 TPSA 28.7 ✓ Ro5 ✓ Clean c1c(cn[nH]1)I

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.