Protein profile

KP13_01870

Spermidine synthase

Genome: KpKP13

Gene: speE AHE46310.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GMP3
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Amino acids 286
Annotations 5
Features 23
PDB binders 7
Druggability 0.951

Overview

Basic information about this protein and its source genome.

Accession
KP13_01870
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
speE AHE46310.1
Status
annotated
Amino acids
286
Structure source
AlphaFold + ColabFold
EC
2.5.1.16
GO
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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0004766 Catalysis of the reaction: S-adenosylmethioninamine + putrescine = 5'-methylthioadenosine + spermidine. GO:0008295 The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
44.0
Human E-value
3.65e-26
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
94.89

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 0.951
Structure A0A0H3GMP3
Pocket Pocket 1
P2Rank 0.939
Structure A0A0H3GMP3
Pocket Pocket 1
ColabFold model
FPocket 0.615 · Pocket 1
P2Rank 0.896 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 83 / 4744 genomes with a hit
Normalized 0.017

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: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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0004766 Catalysis of the reaction: S-adenosylmethioninamine + putrescine = 5'-methylthioadenosine + spermidine.
  • GO:0008295 The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
55 286 FunFam G3DSA:3.40.50.150:FF:000026 Polyamine aminopropyltransferase
17 241 NCBIfam NF037959 fused MFS/spermidine synthase
6 57 Pfam PF17284 Spermidine synthase tetramerisation domain
6 57 InterPro IPR035246 Spermidine synthase, tetramerisation domain
55 285 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
55 285 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
60 239 Pfam PF01564 Spermine/spermidine synthase domain
1 54 Gene3D G3DSA:2.30.140.10 Spermidine synthase, tetramerisation domain
1 54 InterPro IPR037163 Spermidine synthase, tetramerisation domain superfamily
81 191 CDD cd02440 AdoMet_MTases
7 278 NCBIfam TIGR00417 spermidine synthase
7 278 InterPro IPR001045 Spermidine/spermine synthases
7 283 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
7 283 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
5 238 ProSiteProfiles PS51006 Polyamine biosynthesis (PABS) domain profile.
5 238 InterPro IPR030374 Polyamine biosynthesis domain
81 94 ProSitePatterns PS01330 Polyamine biosynthesis (PABS) domain signature.
81 94 InterPro IPR030373 Polyamine biosynthesis domain, conserved site
1 54 FunFam G3DSA:2.30.140.10:FF:000002 Polyamine aminopropyltransferase
4 283 PANTHER PTHR11558 SPERMIDINE/SPERMINE SYNTHASE
4 283 InterPro IPR001045 Spermidine/spermine synthases
6 284 Hamap MF_00198 Polyamine aminopropyltransferase [speE].
6 284 InterPro IPR001045 Spermidine/spermine synthases

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_A0A0H3GMP3
AlphaFold — — full sequence — Viewing
ColabFold KP13_01870
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
1 0.951

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 21.2 0.867
2 0.99 0.005
3 0.96 0.005

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.

61 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
DSH
3RW9
P19623 340.4 Da LogP -0.89 TPSA 145.3 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
HAI
6O65
Q9ZUB3 100.2 Da LogP 0.56 TPSA 27.6 ✓ Ro5 ✓ Clean C1CCC(CC1)[NH3+]
MLI
6O64
O48661 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
MTA
2O05
P19623 297.3 Da LogP -0.61 TPSA 119.3 ✓ Ro5 ✓ Clean CSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)…
PUT
2O06
P19623 88.2 Da LogP -0.32 TPSA 52.0 ✓ Ro5 ✓ Clean C(CCN)CN
S4M
2O0L
P19623 356.5 Da LogP -0.99 TPSA 145.3 ✓ Ro5 ✓ Clean C[S@@H](CCCN)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cn…
SPD
2O07
P19623 145.2 Da LogP -0.34 TPSA 64.1 ✓ Ro5 ✓ Clean C(CCNCCCN)CN

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.