Protein profile

KP13_00350

Malate synthase A

Genome: KpKP13

Gene: aceB AHE46911.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GLT0
Amino acids 533
Annotations 3
Features 20
PDB binders 48
Druggability 0.522

Overview

Basic information about this protein and its source genome.

Accession
KP13_00350
Gene
aceB AHE46911.1
Status
annotated
Amino acids
533
Structure source
AlphaFold + ColabFold

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
96.94

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 0.522
Structure A0A0H3GLT0
Pocket Pocket 2
P2Rank 0.954
Structure A0A0H3GLT0
Pocket Pocket 1
ColabFold model
FPocket 0.654 · Pocket 1
P2Rank 0.798 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 161 / 4744 genomes with a hit
Normalized 0.034

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0004474 Catalysis of the reaction: acetyl-CoA + glyoxylate + H2O = (S)-malate + CoA + H+.
  • 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:0006097 A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
24 532 NCBIfam TIGR01344 malate synthase A
24 532 InterPro IPR006252 Malate synthase A
2 533 PIRSF PIRSF001363 Malate_synth
2 533 InterPro IPR006252 Malate synthase A
412 533 FunFam G3DSA:1.20.1220.12:FF:000001 Malate synthase
12 532 Pfam PF01274 Malate synthase
12 532 InterPro IPR001465 Malate synthase
266 281 ProSitePatterns PS00510 Malate synthase signature.
266 281 InterPro IPR019830 Malate synthase, conserved site
11 532 SUPERFAMILY SSF51645 Malate synthase G
11 532 InterPro IPR011076 Malate synthase superfamily
8 530 PANTHER PTHR42902 MALATE SYNTHASE
8 530 InterPro IPR006252 Malate synthase A
7 411 FunFam G3DSA:3.20.20.360:FF:000001 Malate synthase
2 411 Gene3D G3DSA:3.20.20.360 Malate synthase, domain 3
2 411 InterPro IPR046363 Malate synthase, N-terminal and TIM-barrel domains
24 533 CDD cd00727 malate_synt_A
24 533 InterPro IPR006252 Malate synthase A
412 533 Gene3D G3DSA:1.20.1220.12 Malate synthase, domain III
412 533 InterPro IPR044856 Malate synthase, C-terminal superfamily

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_A0A0H3GLT0
AlphaFold full sequence Viewing
ColabFold KP13_00350
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
2 0.522
1 0.235
13 0.17
20 0.125

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 43.26 0.954
2 5.13 0.194
3 3.48 0.101
4 3.43 0.098
5 3.19 0.087

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.

98 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
040 P9WK17 206.2 Da LogP 1.22 TPSA 71.4 ✓ Ro5 ✓ Clean Cc1ccccc1C(=O)CC(=O)C(=O)O
043 P9WK17 271.1 Da LogP 1.68 TPSA 71.4 ✓ Ro5 ✓ Clean c1cc(cc(c1)Br)C(=O)CC(=O)C(=O)O
1F1 P9WK17 161.2 Da LogP 1.87 TPSA 53.1 ✓ Ro5 ✓ Clean c1cc(cc2c1cc[nH]2)C(=O)O
4WL P9WK17 167.2 Da LogP 1.93 TPSA 53.1 ✓ Ro5 ✓ Clean c1csc2c1[nH]c(c2)C(=O)O
4YZ P9WK17 216.7 Da LogP 2.91 TPSA 37.3 ✓ Ro5 ✓ Clean c1cc(ccc1SCCC(=O)O)Cl
4Z0 P9WK17 226.2 Da LogP 1.07 TPSA 80.7 ✓ Ro5 ✓ Clean c1cc(sc1)C(=O)OC=CC(=O)C(=O)O
4Z1 P9WK17 249.1 Da LogP 1.52 TPSA 78.4 ✓ Ro5 ✓ Clean c1cc(c(cc1Cl)Cl)NNC(=O)C(=O)O
4Z3 P9WK17 243.1 Da LogP 1.85 TPSA 61.7 ✓ Ro5 ✓ Clean c1ccc(c(c1)NC(=O)C=NO)Br
4Z4 P9WK17 209.0 Da LogP 2.83 TPSA 37.3 ✓ Ro5 ✓ Clean c1c(c(cc(c1F)Cl)Cl)C(=O)O
4Z9 P9WK17 205.2 Da LogP 1.16 TPSA 73.3 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)C[C@H](C(=O)O)O
4ZA P9WK17 167.2 Da LogP 1.93 TPSA 53.1 ✓ Ro5 ✓ Clean c1csc2c1cc([nH]2)C(=O)O
4ZC P9WK17 153.6 Da LogP 1.92 TPSA 44.0 ✓ Ro5 ✓ Clean c1cc(c(cc1Cl)C#N)O
4ZD P9WK17 180.2 Da LogP 2.38 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)SC=CC(=O)O
4ZF P9WK17 227.2 Da LogP 1.19 TPSA 73.7 ✓ Ro5 ✓ Clean c1ccc2c(c1)/C(=C\3/C=C(NN3)C(=O)O)/C=N2
4ZU P9WK17 240.1 Da LogP 2.63 TPSA 53.1 ✓ Ro5 ✓ Clean c1cc(cc2c1cc([nH]2)C(=O)O)Br
4ZV P9WK17 161.2 Da LogP 1.87 TPSA 53.1 ✓ Ro5 ✓ Clean c1cc2c(cc[nH]2)cc1C(=O)O
50C P9WK17 191.2 Da LogP 2.11 TPSA 54.7 ✓ Ro5 ✓ Clean Cc1c(n[nH]c1N)c2ccc(cc2)F
52F P9WK17 218.2 Da LogP 0.94 TPSA 83.0 ✓ Ro5 ✓ Clean c1ccc2c(c1)NC(=O)C(=N2)CCC(=O)O
5EQ P9WK17 231.2 Da LogP 1.88 TPSA 90.4 ✓ Ro5 ✓ Clean c1cc2c(cc[nH]2)cc1C(=O)C=C(C(=O)O)O
5ER P9WK17 231.2 Da LogP 1.88 TPSA 90.4 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)C(=O)/C=C(/C(=O)O)\O
5H6 P9WK17 229.6 Da LogP 2.75 TPSA 63.3 ✓ Ro5 ✓ Clean c1cc(sc1c2cc(no2)C(=O)O)Cl
5LA P9WK17 201.6 Da LogP 2.58 TPSA 53.1 ✓ Ro5 ✓ Clean c1c2cc(sc2[nH]c1C(=O)O)Cl
5M2 P9WK17 245.2 Da LogP 2.19 TPSA 90.4 ✓ Ro5 ✓ Clean Cc1c2cc[nH]c2ccc1C(=O)/C=C(/C(=O)O)\O
6MW P9WK17 210.3 Da LogP 0.87 TPSA 62.2 ✓ Ro5 ✓ Clean c1cnccc1[C@H]2N[C@H](CS2)C(=O)O
BQ4 P9WK17 208.2 Da LogP 1.10 TPSA 94.8 ✓ Ro5 ✓ Clean c1cc(cc(c1)O)C(=O)/C=C(/C(=O)O)\O
BSV P9WK17 246.3 Da LogP 2.58 TPSA 74.6 ✓ Ro5 ✓ Clean Cc1ccc(cc1C(=O)/C=C(/C(=O)O)\O)C2CC2
BVS P9WK17 206.2 Da LogP 1.70 TPSA 74.6 ✓ Ro5 ✓ Clean Cc1ccc(cc1)C(=O)/C=C(/C(=O)O)\O
BXS P9WK17 250.2 Da LogP 1.17 TPSA 93.1 ✓ Ro5 ✓ Clean c1cc2c(cc1C(=O)/C=C(/C(=O)O)\O)OCCO2
C0V P9WK17 242.2 Da LogP 2.55 TPSA 74.6 ✓ Ro5 ✓ Clean c1ccc2cc(ccc2c1)C(=O)/C=C(/C(=O)O)\O
D1Y P9WK17 242.6 Da LogP 1.75 TPSA 94.8 ✓ Ro5 ✓ Clean c1cc(c(cc1O)Cl)C(=O)C=C(C(=O)O)O
E9S P9WK17 287.1 Da LogP 1.86 TPSA 94.8 ✓ Ro5 ✓ Clean c1cc(c(c(c1)O)Br)C(=O)C=C(C(=O)O)O
EHV P9WK17 287.1 Da LogP 1.78 TPSA 74.6 ✓ Ro5 ✓ Clean Cc1cccc(c1C(=O)C[C@@H](C(=O)O)O)Br
ENG P9WK17 287.1 Da LogP 1.86 TPSA 94.8 ✓ Ro5 ✓ Clean c1cc(c(cc1O)Br)C(=O)C=C(C(=O)O)O
ENY P9WK17 272.3 Da LogP 2.56 TPSA 83.8 ✓ Ro5 ✓ Clean COc1ccc2cc(ccc2c1)C(=O)/C=C(/C(=O)O)\O
EQA P9WK17 210.2 Da LogP 1.53 TPSA 74.6 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)C=C(C(=O)O)O)F
GLV P9WK17 74.0 Da LogP -0.73 TPSA 54.4 ✓ Ro5 ✓ Clean C(=O)C(=O)O
GXD P9WK17 261.1 Da LogP 2.22 TPSA 71.4 ✓ Ro5 ✓ Clean c1cc(c(c(c1)Cl)C(=O)CC(=O)C(=O)O)Cl
GXG P9WK17 228.1 Da LogP 1.19 TPSA 71.4 ✓ Ro5 ✓ Clean c1cc(c(c(c1)F)C(=O)CC(=O)C(=O)O)F
GXM P9WK17 237.2 Da LogP 1.30 TPSA 117.7 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)/C=C(/C(=O)O)\O)[N+](=O)[O-]
GZV P9WK17 242.2 Da LogP 1.98 TPSA 74.6 ✓ Ro5 ✓ Clean Cc1ccc(c(c1F)C(=O)C=C(C(=O)O)O)F
I92 P9WK17 271.1 Da LogP 1.68 TPSA 71.4 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)CC(=O)C(=O)O)Br
I93 P9WK17 258.6 Da LogP 2.01 TPSA 71.4 ✓ Ro5 ✓ Clean Cc1ccc(c(c1Cl)C(=O)CC(=O)C(=O)O)F
ICO P9WK17 161.2 Da LogP 1.87 TPSA 53.1 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)C(=O)O
LMR P9WK17 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)O)C(=O)O
MLT P9WK17 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
OXL P08997 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=O)[O-])[O-]
PYC P9WK17 110.1 Da LogP -0.62 TPSA 55.9 ✓ Ro5 ✓ Clean c1cc([nH]c1)C(=O)[O-]
XI7 P9WK17 192.2 Da LogP 0.91 TPSA 71.4 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)CC(=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.