Protein profile

VK055_0686

L-2,4-diaminobutyrate decarboxylase

Genome: KpATCC43816

Gene: ddc AIK79309.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GNN7
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Amino acids 490
Annotations 6
Features 10
PDB binders 5
Druggability 0.636

Overview

Basic information about this protein and its source genome.

Accession
VK055_0686
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
ddc AIK79309.1
Status
annotated
Amino acids
490
Structure source
AlphaFold + ColabFold
GO
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0019752 The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-). GO:0016830 Catalysis of the cleavage of C-C bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
48.958
Human E-value
1.62e-23
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
32.277
Localization
Cytoplasmic
ColabFold pLDDT
95.77

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 0.636
Structure A0A0H3GNN7
Pocket Pocket 10
P2Rank 0.715
Structure A0A0H3GNN7
Pocket Pocket 1
ColabFold model
FPocket 0.777 · Pocket 7
P2Rank 0.778 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 72 / 4744 genomes with a hit
Normalized 0.015

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:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0019752 The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
  • GO:0016830 Catalysis of the cleavage of C-C bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.

Sequence Features

Domain/signature hits from InterPro and related databases.

10 records
Show feature table
Start End DB Term Name
109 360 Gene3D G3DSA:3.40.640.10 -
109 360 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
470 490 Coils Coil Coil
65 416 Pfam PF00282 Pyridoxal-dependent decarboxylase conserved domain
65 416 InterPro IPR002129 Pyridoxal phosphate-dependent decarboxylase
16 486 PANTHER PTHR45677 GLUTAMATE DECARBOXYLASE-RELATED
85 482 CDD cd06450 DOPA_deC_like
40 484 Gene3D G3DSA:3.90.1150.170 -
16 487 SUPERFAMILY SSF53383 PLP-dependent transferases
16 487 InterPro IPR015424 Pyridoxal phosphate-dependent transferase

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_A0A0H3GNN7
AlphaFold — — full sequence — Viewing
ColabFold VK055_0686
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
34 0.034
4 0.002
7 0.001
8 0.0

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 17.0 0.715
2 3.79 0.118
3 2.65 0.063
4 1.55 0.019
5 1.4 0.015

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.

55 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
2SU
4OBV
A7B1V0 236.2 Da LogP 1.46 TPSA 79.1 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)C[C@](CF)(C(=O)O)N
3SO
4OBV
A7B1V0 402.3 Da LogP 3.01 TPSA 132.7 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=C/C(=O)Cc2c[nH]c3c2…
ABU
4RLG
D1C7D8 103.1 Da LogP -0.19 TPSA 63.3 ✓ Ro5 ✓ Clean C(CC(=O)O)CN
PLZ
2OKJ
Q99259 334.3 Da LogP 0.66 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNCCCC(=O)O)O
PMP
4RIZ
D1C7D8 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)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.