Protein profile

VK055_0557

1-pyrroline dehydrogenase

Genome: KpATCC43816

Gene: ydcW AIK79180.1 Structure source: AlphaFold + ColabFold UniProt A0A0C7KN36
Amino acids 475
Annotations 8
Features 19
PDB binders 13
Druggability 0.486

Overview

Basic information about this protein and its source genome.

Accession
VK055_0557
Gene
ydcW AIK79180.1
Status
annotated
Amino acids
475
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
54.386
Human E-value
3.63e-11
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
41.822
DEG E-value
5.42e-111
Localization
Cytoplasmic
ColabFold pLDDT
97.88

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 0.486
Structure A0A0C7KN36
Pocket Pocket 21
P2Rank 0.866
Structure A0A0C7KN36
Pocket Pocket 1
ColabFold model
FPocket 0.868 · Pocket 1
P2Rank 0.967 · 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.

2 EC 6 GO

Enzyme Commission (EC)

2

Gene Ontology (GO)

6
  • GO:0016620 Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
  • 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:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
  • GO:0009447 The chemical reactions and pathways resulting in the breakdown of putrescine, 1,4-diaminobutane; putrescine is the metabolic precursor of spermidine and spermine.
  • GO:0019145 Catalysis of the reaction: 4-aminobutanal + NAD+ + H2O = 4-aminobutanoate + NADH + 2 H+.
  • GO:0019477 The chemical reactions and pathways resulting in the breakdown of L-lysine.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
245 252 ProSitePatterns PS00687 Aldehyde dehydrogenases glutamic acid active site.
245 252 InterPro IPR029510 Aldehyde dehydrogenase, glutamic acid active site
249 439 Gene3D G3DSA:3.40.309.10 Aldehyde Dehydrogenase; Chain A, domain 2
249 439 InterPro IPR016163 Aldehyde dehydrogenase, C-terminal
1 474 Hamap MF_01275 Gamma-aminobutyraldehyde dehydrogenase [patD].
1 474 InterPro IPR017749 Gamma-aminobutyraldehyde dehydrogenase
19 464 Gene3D G3DSA:3.40.605.10 Aldehyde Dehydrogenase; Chain A, domain 1
19 464 InterPro IPR016162 Aldehyde dehydrogenase, N-terminal
249 442 FunFam G3DSA:3.40.309.10:FF:000010 Gamma-aminobutyraldehyde dehydrogenase
2 473 SUPERFAMILY SSF53720 ALDH-like
2 473 InterPro IPR016161 Aldehyde/histidinol dehydrogenase
4 473 PANTHER PTHR11699 ALDEHYDE DEHYDROGENASE-RELATED
21 472 CDD cd07092 ALDH_ABALDH-YdcW
21 472 InterPro IPR015657 Aminobutyraldehyde dehydrogenase
14 261 FunFam G3DSA:3.40.605.10:FF:000001 Aldehyde dehydrogenase 1
2 473 NCBIfam TIGR03374 aminobutyraldehyde dehydrogenase
2 473 InterPro IPR017749 Gamma-aminobutyraldehyde dehydrogenase
13 470 Pfam PF00171 Aldehyde dehydrogenase family
13 470 InterPro IPR015590 Aldehyde dehydrogenase 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...

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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_A0A0C7KN36
AlphaFold full sequence Viewing
ColabFold VK055_0557
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
21 0.486

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 16.7 0.785
2 11.82 0.627
3 5.36 0.254
4 1.62 0.026
5 1.39 0.017

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.

117 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
0D8 P17202 75.1 Da LogP -0.67 TPSA 46.2 ✓ Ro5 ✓ Clean C(CN)CO
7PE Q9HTJ1 310.4 Da LogP 0.10 TPSA 75.6 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCO
AE3 P17202 134.2 Da LogP 0.03 TPSA 38.7 ✓ Ro5 ✓ Clean CCOCCOCCO
B3P A0A0H2X0S3 282.3 Da LogP -4.01 TPSA 145.4 1 viol. ✓ Clean C(CNC(CO)(CO)CO)CNC(CO)(CO)CO
BTL P77674 102.2 Da LogP -0.11 TPSA 17.1 ✓ Ro5 ✓ Clean C[N+](C)(C)CC=O
CHT P17202 104.2 Da LogP -0.32 TPSA 20.2 ✓ Ro5 ✓ Clean C[N+](C)(C)CCO
CQY O94788 430.5 Da LogP 3.62 TPSA 79.2 ✓ Ro5 ✓ Clean CCOc1ccsc1C(=O)N2CCN(CC2)c3ccc(c(c3)N4CCCC4)[N+…
CU4 O94788 460.5 Da LogP 4.21 TPSA 104.8 ✓ Ro5 ✓ Clean CS(=O)(=O)c1ccc(cc1)c2c(cn(n2)c3ccc(cc3)C#N)C(=…
DTT Q9HTJ1 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
ETX P17202 90.1 Da LogP 0.02 TPSA 29.5 ✓ Ro5 ✓ Clean CCOCCO
PE4 Q9HTJ1 354.4 Da LogP 0.11 TPSA 84.8 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCO
TOE Q9HTJ1 164.2 Da LogP -0.34 TPSA 47.9 ✓ Ro5 ✓ Clean COCCOCCOCCO
TXE Q9HTJ1 667.5 Da LogP -2.95 TPSA 317.6 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.