Protein profile

KP13_05010

Protein malY

Genome: KpKP13

Gene: malY AHE44815.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GP61
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Amino acids 390
Annotations 5
Features 12
PDB binders 8
Druggability 0.195

Overview

Basic information about this protein and its source genome.

Accession
KP13_05010
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
malY AHE44815.1
Status
annotated
Amino acids
390
Structure source
AlphaFold + ColabFold
EC
4.4.1.13
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:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. 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:0047804 Catalysis of the reaction: S-substituted L-cysteine + H2O = a thiol + NH4+ + pyruvate.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
29.412
Human E-value
6.49e-14
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.23

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 0.195
Structure A0A0H3GP61
Pocket Pocket 2
P2Rank 0.668
Structure A0A0H3GP61
Pocket Pocket 1
ColabFold model
FPocket 0.506 · Pocket 1
P2Rank 0.589 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 91 / 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 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • 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:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
  • 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:0047804 Catalysis of the reaction: S-substituted L-cysteine + H2O = a thiol + NH4+ + pyruvate.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
30 381 Pfam PF00155 Aminotransferase class I and II
30 381 InterPro IPR004839 Aminotransferase, class I/classII
4 386 NCBIfam TIGR04350 PatB family C-S lyase
4 386 InterPro IPR027619 C-S lyase, PatB-like
31 382 CDD cd00609 AAT_like
12 380 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
12 380 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
68 290 Gene3D G3DSA:3.40.640.10 -
68 290 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
1 388 SUPERFAMILY SSF53383 PLP-dependent transferases
1 388 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
2 388 PANTHER PTHR43525 PROTEIN MALY

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_A0A0H3GP61
AlphaFold — — full sequence — Viewing
ColabFold KP13_05010
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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 8.49 0.453
2 1.52 0.022
3 1.43 0.019
4 0.74 0.002
5 0.58 0.0

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.

58 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
C6P
2R5C
Q17CS8 352.3 Da LogP 0.18 TPSA 149.2 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CS)C(=O)O)O
HCI
1V2F
Q75WK2 150.2 Da LogP 1.70 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)CCC(=O)O
KMT
1V2E
Q75WK2 148.2 Da LogP 0.39 TPSA 54.4 ✓ Ro5 ✓ Clean CSCCC(=O)C(=O)O
KYN
3E2Z
Q71RI9 208.2 Da LogP 0.25 TPSA 106.4 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)C[C@@H](C(=O)O)N)N
PLS
3B1D
A6BMJ3 336.2 Da LogP -0.76 TPSA 169.4 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CO)C(=O)O)O
PMP
1YIY
Q17CS8 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
PPG
1C7O
Q56257 389.3 Da LogP 0.22 TPSA 184.8 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)C/N=C(\C=C\OCCN)/C(=O)…
QLP
2R5E
Q17CS8 377.3 Da LogP -0.49 TPSA 192.3 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CCC(=O)N)C(=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.