Protein profile

KP13_01814

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Genome: KpKP13

Gene: AHE46254.1 dapD Structure source: AlphaFold + ColabFold UniProt A0A0H3GMV1
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Amino acids 274
Annotations 7
Features 18
PDB binders 5
Druggability 0.532

Overview

Basic information about this protein and its source genome.

Accession
KP13_01814
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE46254.1 dapD
Status
annotated
Amino acids
274
Structure source
AlphaFold + ColabFold
EC
2.3.1.117
GO
GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate. 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:0008666 Catalysis of the reaction: (S)-2,3,4,5-tetrahydrodipicolinate + H2O + succinyl-CoA = L-2-succinylamino-6-oxopimelate + CoA. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0016779 Catalysis of the transfer of a nucleotidyl group from one compound (donor) to another (acceptor). GO:0019877 OBSOLETE. The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
98.905
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.05

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 0.532
Structure A0A0H3GMV1
Pocket Pocket 14
P2Rank 0.188
Structure A0A0H3GMV1
Pocket Pocket 1
ColabFold model
FPocket 0.408 · Pocket 9
P2Rank 0.209 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 230 / 4744 genomes with a hit
Normalized 0.048

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:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
  • 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:0008666 Catalysis of the reaction: (S)-2,3,4,5-tetrahydrodipicolinate + H2O + succinyl-CoA = L-2-succinylamino-6-oxopimelate + CoA.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0016779 Catalysis of the transfer of a nucleotidyl group from one compound (donor) to another (acceptor).
  • GO:0019877 OBSOLETE. The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
1 70 Gene3D G3DSA:1.10.166.10 -
1 70 InterPro IPR037133 Tetrahydrodipicolinate-N-succinyltransferase, N-terminal domain superfamily
3 69 Pfam PF14805 Tetrahydrodipicolinate N-succinyltransferase N-terminal
3 69 InterPro IPR023180 Tetrahydrodipicolinate-N-succinyltransferase, chain A, domain 1
175 209 Pfam PF14602 Hexapeptide repeat of succinyl-transferase
175 209 InterPro IPR001451 Hexapeptide repeat
1 256 SUPERFAMILY SSF51161 Trimeric LpxA-like enzymes
1 256 InterPro IPR011004 Trimeric LpxA-like superfamily
1 272 Hamap MF_00811 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase [dapD].
1 272 InterPro IPR005664 Tetrahydrodipicolinate N-succinyltransferase, transferase hexapeptide repeat family
88 256 FunFam G3DSA:2.160.10.10:FF:000004 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
134 162 ProSitePatterns PS00101 Hexapeptide-repeat containing-transferases signature.
134 162 InterPro IPR018357 Hexapeptide transferase, conserved site
102 239 CDD cd03350 LbH_THP_succinylT
1 273 PANTHER PTHR19136 MOLYBDENUM COFACTOR GUANYLYLTRANSFERASE
3 273 NCBIfam TIGR00965 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
3 273 InterPro IPR005664 Tetrahydrodipicolinate N-succinyltransferase, transferase hexapeptide repeat family
88 256 Gene3D G3DSA:2.160.10.10 Hexapeptide repeat proteins

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_A0A0H3GMV1
AlphaFold — — full sequence — Viewing
ColabFold KP13_01814
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
14 0.532

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 3.67 0.139

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.

55 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
26P
3TDT
P56220 189.2 Da LogP -0.78 TPSA 117.7 ✓ Ro5 ✓ Clean C(C[C@@H](C(=O)O)N)CC(=O)C(=O)O
NPI
1KGQ
P56220 175.2 Da LogP 0.04 TPSA 100.6 ✓ Ro5 ✓ Clean C(CCC(=O)O)C[C@@H](C(=O)O)N
PML
1KGT
P56220 160.2 Da LogP 1.11 TPSA 74.6 ✓ Ro5 ✓ Clean C(CCC(=O)O)CCC(=O)O
SCA
1KGT
P56220 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](…
SCO
1KGQ
P56220 850.6 Da LogP -2.61 TPSA 413.0 3 viol. ✓ Clean CC(C)(CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H](…

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.