Protein profile

KP13_04866

Adenylosuccinate lyase

Genome: KpKP13

Gene: AHE45226.1 purB Structure source: AlphaFold + ColabFold UniProt A0A0H3GVM8
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Amino acids 456
Annotations 9
Features 28
PDB binders 7
Druggability 0.248

Overview

Basic information about this protein and its source genome.

Accession
KP13_04866
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE45226.1 purB
Status
annotated
Amino acids
456
Structure source
AlphaFold + ColabFold
EC
4.3.2.2
GO
GO:0009152 The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. 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:0004018 Catalysis of the reaction: N6-(1,2-dicarboxyethyl)AMP = fumarate + AMP. GO:0006188 The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0070626 Catalysis of the reaction: (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
23.247
Human E-value
5.01e-07
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
94.079
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.82

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 0.248
Structure A0A0H3GVM8
Pocket Pocket 3
P2Rank 0.116
Structure A0A0H3GVM8
Pocket Pocket 1
ColabFold model
FPocket 0.145 · Pocket 7
P2Rank 0.071 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 598 / 4744 genomes with a hit
Normalized 0.126

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0009152 The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
  • 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:0004018 Catalysis of the reaction: N6-(1,2-dicarboxyethyl)AMP = fumarate + AMP.
  • GO:0006188 The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0070626 Catalysis of the reaction: (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide.
  • GO:0044208 The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from inosine 5'-monophosphate (IMP).
  • GO:0006189 The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
12 455 NCBIfam TIGR00928 adenylosuccinate lyase
12 455 InterPro IPR004769 Adenylosuccinate lyase
23 446 CDD cd01598 PurB
294 303 ProSitePatterns PS00163 Fumarate lyases signature.
294 303 InterPro IPR020557 Fumarate lyase, conserved site
14 312 Pfam PF00206 Lyase
14 312 InterPro IPR022761 Fumarate lyase, N-terminal
382 445 Gene3D G3DSA:1.10.40.30 -
118 384 FunFam G3DSA:1.20.200.10:FF:000004 Adenylosuccinate lyase
118 449 Gene3D G3DSA:1.20.200.10 Fumarase/aspartase (Central domain)
382 445 FunFam G3DSA:1.10.40.30:FF:000004 Adenylosuccinate lyase
10 454 SUPERFAMILY SSF48557 L-aspartase-like
10 454 InterPro IPR008948 L-Aspartase-like
163 181 PRINTS PR00149 Fumarate lyase superfamily signature
163 181 InterPro IPR000362 Fumarate lyase family
294 310 PRINTS PR00149 Fumarate lyase superfamily signature
294 310 InterPro IPR000362 Fumarate lyase family
117 135 PRINTS PR00149 Fumarate lyase superfamily signature
117 135 InterPro IPR000362 Fumarate lyase family
251 278 PRINTS PR00149 Fumarate lyase superfamily signature
251 278 InterPro IPR000362 Fumarate lyase family
1 117 Gene3D G3DSA:1.10.275.10 -
1 117 InterPro IPR024083 Fumarase/histidase, N-terminal
331 445 Pfam PF08328 Adenylosuccinate lyase C-terminal
331 445 InterPro IPR013539 Adenylosuccinate lyase PurB, C-terminal
1 117 FunFam G3DSA:1.10.275.10:FF:000003 Adenylosuccinate lyase
2 454 PANTHER PTHR43411 ADENYLOSUCCINATE LYASE
2 454 InterPro IPR047136 Adenylosuccinate lyase PurB, bacteria

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

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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_A0A0H3GVM8
AlphaFold — — full sequence — Viewing
ColabFold KP13_04866
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
3 0.248

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 2.17 0.051
2 1.58 0.025
3 1.04 0.006
4 0.92 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.

57 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
2SA
2PTR
P0AB89 463.3 Da LogP -2.11 TPSA 246.7 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
DTT
1RE5
Q88N37 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
FUM
2PTQ
P0AB89 116.1 Da LogP -0.29 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)\C(=O)O
MLI
2PFM
A0A6L8PR48 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
N2P
4NSL
Q8ZPZ6 102.2 Da LogP 0.07 TPSA 52.0 ✓ Ro5 ✓ Clean C(CCN)CCN
OXL
2X75
Q7A0G9 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=O)[O-])[O-]
SIN
4EEI
Q5NIQ1 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=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.