Protein profile

KP13_04916

Aminodeoxychorismate lyase

Genome: KpKP13

Gene: AHE45276.1 pabC Structure source: AlphaFold + ColabFold UniProt A0A0H3GRH7
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Amino acids 269
Annotations 7
Features 17
PDB binders 7
Druggability 0.407

Overview

Basic information about this protein and its source genome.

Accession
KP13_04916
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE45276.1 pabC
Status
annotated
Amino acids
269
Structure source
AlphaFold + ColabFold
EC
4.1.3.38
GO
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:0046656 The chemical reactions and pathways resulting in the formation of folic acid, pteroylglutamic acid. 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:0008696 Catalysis of the reaction: 4-amino-4-deoxychorismate = 4-aminobenzoate + H+ + pyruvate. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0008153 The chemical reactions and pathways resulting in the formation of 4-aminobenzoate, an intermediate in the synthesis of folic acid, a compound which some organisms, e.g. prokaryotes, eukaryotic microbes, and plants, can synthesize de novo. Others, notably mammals, cannot. In yeast, it is present as a factor in the B complex of vitamins.

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 (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.19

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 0.407
Structure A0A0H3GRH7
Pocket Pocket 4
P2Rank 0.526
Structure A0A0H3GRH7
Pocket Pocket 1
ColabFold model
FPocket 0.267 · Pocket 9
P2Rank 0.643 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 92 / 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 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • 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:0046656 The chemical reactions and pathways resulting in the formation of folic acid, pteroylglutamic acid.
  • 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:0008696 Catalysis of the reaction: 4-amino-4-deoxychorismate = 4-aminobenzoate + H+ + pyruvate.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008153 The chemical reactions and pathways resulting in the formation of 4-aminobenzoate, an intermediate in the synthesis of folic acid, a compound which some organisms, e.g. prokaryotes, eukaryotic microbes, and plants, can synthesize de novo. Others, notably mammals, cannot. In yeast, it is present as a factor in the B complex of vitamins.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
112 268 Gene3D G3DSA:3.20.10.10 -
112 268 InterPro IPR043132 Branched-chain-amino-acid aminotransferase-like, C-terminal
3 262 NCBIfam TIGR03461 aminodeoxychorismate lyase
3 262 InterPro IPR017824 Aminodeoxychorismate lyase, class IV
12 251 PANTHER PTHR42743 AMINO-ACID AMINOTRANSFERASE
16 265 CDD cd01559 ADCL_like
16 265 InterPro IPR017824 Aminodeoxychorismate lyase, class IV
173 202 ProSitePatterns PS00770 Aminotransferases class-IV signature.
173 202 InterPro IPR018300 Aminotransferase, class IV, conserved site
24 247 Pfam PF01063 Amino-transferase class IV
24 247 InterPro IPR001544 Aminotransferase class IV
1 111 FunFam G3DSA:3.30.470.10:FF:000007 Aminodeoxychorismate lyase
2 263 SUPERFAMILY SSF56752 D-aminoacid aminotransferase-like PLP-dependent enzymes
2 263 InterPro IPR036038 Aminotransferase-like, PLP-dependent enzymes
1 111 Gene3D G3DSA:3.30.470.10 -
1 111 InterPro IPR043131 Branched-chain-amino-acid aminotransferase-like, N-terminal
112 267 FunFam G3DSA:3.20.10.10:FF:000002 D-alanine aminotransferase

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_A0A0H3GRH7
AlphaFold — — full sequence — Viewing
ColabFold KP13_04916
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
4 0.407
3 0.254

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 5.2 0.242
2 2.61 0.075
3 1.84 0.036
4 1.47 0.02

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.

70 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
AKG
5E25
A0A0A7GJ30 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
DCS
1I2L
P28305 333.2 Da LogP -0.78 TPSA 150.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2CONC2=O)O
PDD
3DAA
P19938 320.2 Da LogP 0.27 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](C)C(=O)O)O
PMP
1A0G
P19938 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
PSZ
3LQS
P19938 374.3 Da LogP 2.08 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNc2cc(sc2)C(=O)O)O
PXG
5MR0
O29329 368.3 Da LogP 2.02 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNc2cccc(c2)C(=O)O)O
TAM
5MQZ
O29329 163.2 Da LogP -1.17 TPSA 86.7 ✓ Ro5 ✓ Clean C(CO)C(CCO)(CCO)N

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.