Protein profile

KP13_00203

putative 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase

Genome: KpKP13

Gene: AHE42117.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H4H3
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Amino acids 397
Annotations 10
Features 19
PDB binders 33
Druggability 0.193

Overview

Basic information about this protein and its source genome.

Accession
KP13_00203
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42117.1
Status
annotated
Amino acids
397
Structure source
AlphaFold + ColabFold
EC
2.3.1.29
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:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. 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:0006567 The chemical reactions and pathways resulting in the breakdown of L-threonine. GO:0008890 Catalysis of the reaction: acetyl-CoA + glycine = L-2-amino-3-oxobutanoate + CoA.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
55.385
Human E-value
1.78e-149
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
98.23

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 0.193
Structure A0A0H3H4H3
Pocket Pocket 2
P2Rank 0.759
Structure A0A0H3H4H3
Pocket Pocket 1
ColabFold model
FPocket 0.174 · Pocket 6
P2Rank 0.629 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 710 / 4744 genomes with a hit
Normalized 0.15

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • 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:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
  • 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:0006567 The chemical reactions and pathways resulting in the breakdown of L-threonine.
  • GO:0008890 Catalysis of the reaction: acetyl-CoA + glycine = L-2-amino-3-oxobutanoate + CoA.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0016874 Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient.
  • GO:0019518 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-threonine (the L-enantiomer of 2-amino-3-hydroxybutyric acid) to form 2-amino-3-oxobutanoate, which is subsequently converted to glycine.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
294 386 FunFam G3DSA:3.90.1150.10:FF:000004 2-amino-3-ketobutyrate coenzyme A ligase
240 249 ProSitePatterns PS00599 Aminotransferases class-II pyridoxal-phosphate attachment site.
240 249 InterPro IPR001917 Aminotransferase, class-II, pyridoxal-phosphate binding site
2 394 Hamap MF_00985 2-amino-3-ketobutyrate coenzyme A ligase [kbl].
2 394 InterPro IPR011282 2-amino-3-ketobutyrate coenzyme A ligase
57 295 FunFam G3DSA:3.40.640.10:FF:000006 5-aminolevulinate synthase, mitochondrial
14 388 PANTHER PTHR13693 CLASS II AMINOTRANSFERASE/8-AMINO-7-OXONONANOATE SYNTHASE
39 387 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
39 387 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
57 295 Gene3D G3DSA:3.40.640.10 -
57 295 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
42 386 Pfam PF00155 Aminotransferase class I and II
42 386 InterPro IPR004839 Aminotransferase, class I/classII
5 396 NCBIfam TIGR01822 glycine C-acetyltransferase
5 396 InterPro IPR011282 2-amino-3-ketobutyrate coenzyme A ligase
4 395 SUPERFAMILY SSF53383 PLP-dependent transferases
4 395 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
41 390 CDD cd06454 KBL_like
150 170 Coils Coil Coil

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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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_A0A0H3H4H3
AlphaFold — — full sequence — Viewing
ColabFold KP13_00203
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 11.65 0.619
2 2.92 0.094
3 1.44 0.019
4 1.41 0.018

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.

84 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
2BK
7BXQ
Q0K313 350.3 Da LogP -0.37 TPSA 169.4 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]([C@H](C)O)C(=…
AKB
1FC4
P0AB77 117.1 Da LogP -1.01 TPSA 80.4 ✓ Ro5 ✓ Clean CC(=O)[C@@H](C(=O)O)N
F9X
7BXR
Q0K313 364.3 Da LogP 0.02 TPSA 169.4 1 viol. ✓ Clean CC[C@H]([C@@H](C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O…
HR5
5QR1
P22557 207.3 Da LogP 1.26 TPSA 46.9 ✓ Ro5 ✓ Clean Cc1c(cnn1C)C(=O)NCC2CCC2
J4Q
5QRD
P22557 243.3 Da LogP 0.79 TPSA 64.8 ✓ Ro5 ✓ Clean CS(=O)(=O)c1nccn1Cc2cscn2
JHP
5QQS
P22557 227.7 Da LogP 1.75 TPSA 46.9 ✓ Ro5 ✓ Clean Cn1cc(c(n1)C(=O)NC2CCCC2)Cl
JO1
5QR3
P22557 221.3 Da LogP 1.41 TPSA 46.9 ✓ Ro5 ✓ Clean Cn1c(ccn1)C(=O)NCc2cccs2
K0V
5QR6
P22557 242.3 Da LogP 1.38 TPSA 58.6 ✓ Ro5 ✓ Clean CC(C)(C)NC(=O)N1CCC(CC1)C(=O)OC
LUY
5QR7
P22557 237.3 Da LogP 3.22 TPSA 40.7 ✓ Ro5 ✓ Clean c1ccc(cc1)CCNc2[nH]c3ccccc3n2
NSJ
5QQQ
P22557 209.3 Da LogP 1.94 TPSA 23.5 ✓ Ro5 ✓ Clean c1cc(cc(c1)O)CN2CCSCC2
NSV
5QQR
P22557 197.3 Da LogP 0.86 TPSA 28.2 ✓ Ro5 ✓ Clean Cc1ncc(s1)CN2CCNCC2
NT7
5QQT
P22557 248.3 Da LogP 1.57 TPSA 41.6 ✓ Ro5 ✓ Clean Cc1cccc(c1C)NC(=O)CN2CCOCC2
NTG
5QR2
P22557 203.2 Da LogP 1.18 TPSA 49.2 ✓ Ro5 ✓ Clean c1cc(ncc1N2CCCOCC2)C#N
NTV
5QQV
P22557 239.7 Da LogP 2.77 TPSA 38.3 ✓ Ro5 ✓ Clean Cc1c(cccc1Cl)NC(=O)[C@@H]2CCCO2
NU4
5QQW
P22557 202.2 Da LogP 2.24 TPSA 55.1 ✓ Ro5 ✓ Clean Cc1c(cco1)C(=O)Nc2ccncc2
NUA
5QQX
P22557 193.2 Da LogP 1.64 TPSA 46.9 ✓ Ro5 ✓ Clean CCn1cc(cn1)NC(=O)C2CCC2
NUG
5QQY
P22557 199.3 Da LogP 1.12 TPSA 23.5 ✓ Ro5 ✓ Clean C1CN(CCC1O)CC2=CCSC2
NUJ
5QQZ
P22557 207.3 Da LogP 1.05 TPSA 49.2 ✓ Ro5 ✓ Clean Cc1cc(nc(n1)C)N(C)C2CC(C2)O
NUM
5QR0
P22557 242.3 Da LogP 1.76 TPSA 62.2 ✓ Ro5 ✓ Clean c1ccnc(c1)C(=O)NCCc2ccc(cc2)O
NUY
5QR4
P22557 238.4 Da LogP 1.91 TPSA 23.6 ✓ Ro5 ✓ Clean CC(C)N1CCN(CC1)C(=O)c2cccs2
NV7
5QR5
P22557 244.3 Da LogP 0.36 TPSA 53.8 ✓ Ro5 ✓ Clean CS(=O)(=O)N1CCN(CC1)Cc2ccco2
NVD
5QR8
P22557 217.3 Da LogP 1.09 TPSA 46.0 ✓ Ro5 Alert CN(C)c1ccc(cc1)CNn2cnnc2
NVJ
5QR9
P22557 179.2 Da LogP 1.93 TPSA 38.3 ✓ Ro5 ✓ Clean CCOC(=O)NCc1ccccc1
NVM
5QRA
P22557 222.3 Da LogP 2.53 TPSA 33.2 ✓ Ro5 ✓ Clean C[C@H]1CCN(C=CC1)C(=O)c2cscn2
NVY
5QRB
P22557 222.3 Da LogP 2.72 TPSA 15.3 ✓ Ro5 ✓ Clean CCN1CCC(CC1)Nc2ccccc2F
NW4
5QRC
P22557 225.3 Da LogP 2.21 TPSA 29.5 ✓ Ro5 ✓ Clean C1CCC(CC1)CCC(=O)N2CCOCC2
NW7
5QRE
P22557 235.2 Da LogP 2.09 TPSA 81.2 ✓ Ro5 ✓ Clean CCc1c(c(on1)C)C(=O)Nc2cc(on2)C
PE3
5TXT
P09950 634.8 Da LogP -0.81 TPSA 160.5 2 viol. ✓ Clean C(COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO)O
PLG
7BXS
Q0K313 306.2 Da LogP -0.12 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNCC(=O)O)O
PLS
2W8J
Q93UV0 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
2XBN
Q93UV0 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
SCA
2BWO
P18079 867.6 Da LogP -1.47 TPSA 400.9 3 viol. ✓ Clean CC(C)(CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H](…
SIN
2BWN
P18079 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.