Protein target profile

PA1330

short-chain dehydrogenase

Genome: NC_002516.2

Gene: PA1330 3D evidence: AlphaFold DB model UniProt Q9I414
Length 259
Pocket druggability 0.711
Ligand records 166
EC / GO 0 / 1
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

4 signals
How to read this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal TPW pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Overview

Basic information about this protein and its source genome.

Accession
PA1330
Gene
PA1330
Status
annotated
Amino acids
259
3D evidence
AlphaFold DB model

Target profile

Computed evidence for target prioritization.

Human off-target
Hit
Human identity (%)
38.532
Human E-value
1.75e-18
Gut microbiome off-target
Hit
Essential (DEG)
N
Localization
Cytoplasmic

Selected pocket evidence

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.711
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MKQKRILVTGAGSGFGREVALRLAARGHRTIAGVRGAGQAADLREEAGRRGVPLRVETLDITVAADRERAWEWDIDVLLNNAGSAEAGASAEIPLELVRALFETNVFANLELTQGFVRRMVEQKRGGKVLFVSSIAGLITGPYTGPYCASKHALEAFAEALHAELKPFGIQVGTINPGPYQTGFNDRMMETWKRWYDPQRHFTDHSGVRFPFEQYDPEEMIARMVELAEADEGPFRTLLPQAFVEVVKDEQAQAWQRRL

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

1
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
2 251 PANTHER PTHR42901 ALCOHOL DEHYDROGENASE
4 178 SMART SM00822 This enzymatic domain is part of bacterial polyketide synthases and catalyses the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group.
3 258 Gene3D G3DSA:3.40.50.720 -
73 84 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
73 84 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
147 166 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
147 166 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
168 185 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
168 185 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
5 22 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
5 22 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
121 137 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
121 137 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
4 244 CDD cd05374 17beta-HSD-like_SDR_c
2 232 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
2 232 InterPro IPR036291 NAD(P)-binding domain superfamily
147 166 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature
127 135 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature
127 135 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
73 84 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature
134 162 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature.
134 162 InterPro IPR020904 Short-chain dehydrogenase/reductase, conserved site
4 188 Pfam PF00106 short chain dehydrogenase
4 188 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

3D visualization script Full viewer

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Structural evidence

0 + 1

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB PA1330
AlphaFold DB full sequence Viewing
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1
0.711
Show in viewer
Site 2 FPocket #4
0.524
Show in viewer
Site 3 FPocket #7
0.278
Show in viewer

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.

166 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 166 via homologs
Structural ligands 16 0 loaded crystals
Bioactive compounds 100 50 ZINC proposed compounds
Drug-like & clean 102 4 PAINS alerts
Best available ligand signal
5SD PDB via homolog 288.4 Da · LogP 4.17 · TPSA 34.1 Open detail RCSB PDB
Detail RCSB PDB 5SD PDB via homolog
Detail RCSB PDB AND PDB via homolog
Detail RCSB PDB AOM PDB via homolog
Detail RCSB PDB ASD PDB via homolog

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
5SD RCSB PDB P14061 288.4 Da LogP 4.17 TPSA 34.1 ✓ Ro5 ✓ Clean C[C@]12CCC(=O)C[C@@H]1CC[C@@H]3[C@@H]2CC[C@]4([…
AND RCSB PDB P14061 288.4 Da LogP 3.88 TPSA 37.3 ✓ Ro5 ✓ Clean C[C@]12CC[C@H]3[C@H]([C@@H]1CCC2=O)CC=C4[C@@]3(…
AOM RCSB PDB P14061 292.5 Da LogP 3.75 TPSA 40.5 ✓ Ro5 ✓ Clean C[C@]12CC[C@@H](C[C@@H]1CC[C@@H]3[C@@H]2CC[C@]4…
ASD RCSB PDB P14061 286.4 Da LogP 4.09 TPSA 34.1 ✓ Ro5 ✓ Clean C[C@]12CCC(=O)C=C1CC[C@@H]3[C@@H]2CC[C@]4([C@H]…
DHT RCSB PDB P14061 290.4 Da LogP 3.96 TPSA 37.3 ✓ Ro5 ✓ Clean C[C@]12CCC(=O)C[C@@H]1CC[C@@H]3[C@@H]2CC[C@]4([…
E2B RCSB PDB P14061 405.5 Da LogP 4.18 TPSA 83.5 ✓ Ro5 ✓ Clean C[C@]12CC[C@@H]3c4ccc(cc4CC[C@H]3[C@@H]1C[C@@H]…
EM9 RCSB PDB P14061 560.3 Da LogP 8.21 TPSA 60.8 2 viol. ✓ Clean CCCCN(C)C(=O)CCCCCCCCCC[C@@H]1Cc2cc(ccc2[C@@H]3…
EMO RCSB PDB P16544 270.2 Da LogP 1.89 TPSA 94.8 ✓ Ro5 Alert Cc1cc2c(c(c1)O)C(=O)c3c(cc(cc3O)O)C2=O
EQI RCSB PDB P14061 268.4 Da LogP 3.74 TPSA 37.3 ✓ Ro5 ✓ Clean C[C@]12CC[C@@H]3c4ccc(cc4CC=C3[C@@H]1CCC2=O)O
EST RCSB PDB P14061 272.4 Da LogP 3.61 TPSA 40.5 ✓ Ro5 ✓ Clean C[C@]12CC[C@@H]3c4ccc(cc4CC[C@H]3[C@@H]1CC[C@@H…
F0A RCSB PDB P14061 435.6 Da LogP 4.19 TPSA 92.8 ✓ Ro5 ✓ Clean C[C@]12CC[C@@H]3c4cc(c(cc4CC[C@H]3[C@@H]1C[C@@H…
F0D RCSB PDB P14061 496.5 Da LogP 5.41 TPSA 63.3 1 viol. ✓ Clean C[C@]12CC[C@@H]3c4ccc(cc4CC[C@H]3[C@@H]1C[C@@H]…
HYC RCSB PDB P14061 677.8 Da LogP 4.54 TPSA 186.1 2 viol. ✓ Clean C[C@]12CC[C@@H]3c4ccc(cc4CC[C@H]3[C@@H]1C[C@@H]…
ISZ RCSB PDB P16544 135.1 Da LogP 1.25 TPSA 66.2 ✓ Ro5 Alert [H]/N=N/C(=O)c1ccncc1
J3Z RCSB PDB P14061 270.4 Da LogP 3.82 TPSA 37.3 ✓ Ro5 ✓ Clean C[C@]12CC[C@@H]3c4ccc(cc4CC[C@H]3[C@@H]1CCC2=O)O
TES RCSB PDB P14061 288.4 Da LogP 3.88 TPSA 37.3 ✓ Ro5 ✓ Clean C[C@]12CC[C@H]3[C@H]([C@@H]1CC[C@@H]2O)CCC4=CC(…

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.