Protein target profile

PA1523

xanthine dehydrogenase

Genome: NC_002516.2

Gene: PA1523 xdhB 3D evidence: AlphaFold DB model UniProt Q9I3J0
Length 799
Pocket druggability 0.696
Ligand records 170
EC / GO 0 / 4
Target summary

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

3 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
PA1523
Gene
PA1523 xdhB
Status
annotated
Amino acids
799
3D evidence
AlphaFold DB model

Target profile

Computed evidence for target prioritization.

Human off-target
Hit
Human identity (%)
49.682
Human E-value
1.2200000000000001e-43
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 0.696
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MSNHRKPHKSQEELADLFRAELTTGVGRSVKHESAPKHVSGEAIYIDDRLEFPNQLHVYARLSERAHARITRLDVTPCYQFPGVAIALTAADVPGQLDIGPVVAGDPLLADGKVEYVGQMVLAVAADSLETARKAAMAAIVEYEDLEPVLDVVEALRKRHFVLDSHQHRIGDSAAALAGAPHRLQGTLHIGGQEHFYLETQISSVMPSEDGGMIVYCSTQNPTEVQKLVAEVLGVSFNRIVIDMRRMGGGFGGKETQAAAPACLCAVVAYHTGRPAKMRLPRMEDMQITGKRHPFYVEYDVGFDDDGRLHGIQIDLAGNCGYSPDLSGSIVDRAMFHSDNAYFLGNATINGHRCKTNTASNTAYRGFGGPQGMVAIEEIMDAVARSLGKDPLEVRKLNYYGKDERNVTHYHQTVEHNLLAEMTAELEASSEYARRREEIRAFNAASPVLKKGLALTPVKFGISFTATFLNQAGALIHIYTDGSIHLNHGGTEMGQGLNTKVAQVVAEVFQVDVERIQITATNTDKVPNTSPTAASSGTDLNGKAAQNAAETIKRRLVEFAARHWKVSEEDIEFRNNQVRIRELILPFEELIQQAYFGQVSLSSTGFYRTPKIFYDREQARGRPFYYFAYGAACSEVIVDTLTGEYRMLRTDILHDVGDSLNPAIDIGQVEGGFVQGMGWLTMEELVWNAKGKLMTSGPASYKIPAVADMPLDLRVKLLENRKNPEQTVFHSKAVGEPPFMLGISVWCAIKDAVASLADYRAQPAIDAPATPERVLWGVEQMRRLKAAQAQAADAAVEPA

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0005506 Binding to an iron (Fe) ion.
  • GO:0030151 Binding to a molybdenum ion (Mo).
  • 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
40 146 Pfam PF01315 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
40 146 InterPro IPR000674 Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead
24 148 SUPERFAMILY SSF54665 CO dehydrogenase molybdoprotein N-domain-like
24 148 InterPro IPR036856 Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily
169 402 Gene3D G3DSA:3.30.365.10 Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
195 289 Gene3D G3DSA:3.30.365.10 Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
426 710 Pfam PF20256 Molybdopterin cofactor-binding domain
426 710 InterPro IPR046867 Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain
466 612 FunFam G3DSA:3.30.365.10:FF:000002 Xanthine dehydrogenase oxidase
25 774 PANTHER PTHR45444 XANTHINE DEHYDROGENASE
25 774 InterPro IPR016208 Aldehyde oxidase/xanthine dehydrogenase
429 774 Gene3D G3DSA:3.30.365.10 Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
148 780 SUPERFAMILY SSF56003 Molybdenum cofactor-binding domain
148 780 InterPro IPR037165 Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily
40 147 SMART SM01008 Ald_Xan_dh_C_2
40 147 InterPro IPR000674 Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead
26 782 NCBIfam TIGR02965 xanthine dehydrogenase molybdopterin binding subunit
26 782 InterPro IPR014309 Xanthine dehydrogenase, molybdopterin binding subunit
466 624 Gene3D G3DSA:3.30.365.10 Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
11 146 Gene3D G3DSA:3.90.1170.50 Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead
522 541 MobiDBLite mobidb-lite consensus disorder prediction
167 399 Pfam PF02738 Molybdopterin cofactor-binding domain
167 399 InterPro IPR008274 Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain
195 289 FunFam G3DSA:3.30.365.10:FF:000001 Xanthine dehydrogenase oxidase

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 PA1523
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
0.696
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.

170 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 170 via homologs
Structural ligands 20 0 loaded crystals
Bioactive compounds 100 50 ZINC proposed compounds
Drug-like & clean 160 8 PAINS alerts
Best available ligand signal
141 PDB via homolog 152.1 Da · LogP -1.11 · TPSA 94.4 Open detail RCSB PDB
Detail RCSB PDB 141 PDB via homolog
Detail RCSB PDB 290 PDB via homolog
Detail RCSB PDB FES PDB via homolog
Detail RCSB PDB FYO 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
141 RCSB PDB O54051 152.1 Da LogP -1.11 TPSA 94.4 ✓ Ro5 ✓ Clean C1=C2C(=NC(=O)NC2=O)NN1
290 RCSB PDB P80457 150.1 Da LogP -0.05 TPSA 74.4 ✓ Ro5 ✓ Clean CC1=NC(=O)Nc2c1nc[nH]2
FES RCSB PDB P80457 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
FYO RCSB PDB P80457 296.2 Da LogP -0.54 TPSA 144.4 ✓ Ro5 ✓ Clean C1C(=CC(=O)NC1=O)c2[nH]nc(n2)C3=CC(=O)NC(=C3)C#N
FYX RCSB PDB P80457 248.2 Da LogP 1.80 TPSA 91.1 ✓ Ro5 ✓ Clean c1cnccc1c2[nH]nc(n2)c3ccnc(c3)C#N
GUN RCSB PDB P80457 151.1 Da LogP -0.77 TPSA 100.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)C(=O)NC(=N2)N
HHR RCSB PDB O54051 193.2 Da LogP -1.21 TPSA 117.8 ✓ Ro5 ✓ Clean c1c(nc2c(n1)N=C(NC2=O)N)CO
HPA RCSB PDB P80457 136.1 Da LogP -0.35 TPSA 74.4 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)N=CNC2=O
I3A RCSB PDB P80457 145.2 Da LogP 1.98 TPSA 32.9 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)C=O
LUZ RCSB PDB P80457 164.1 Da LogP -0.99 TPSA 91.5 ✓ Ro5 ✓ Clean c1cnc2c(n1)C(=O)NC(=O)N2
MOM RCSB PDB P80457 144.9 Da LogP -0.80 TPSA 54.4 ✓ Ro5 ✓ Clean O[Mo](=O)=O
MOS RCSB PDB P80457 161.0 Da LogP 0.14 TPSA 34.1 ✓ Ro5 ✓ Clean O=[Mo](=O)S
MTE RCSB PDB P80457 395.4 Da LogP -0.54 TPSA 171.8 1 viol. ✓ Clean C([C@@H]1C(=C([C@H]2[C@@H](O1)NC3=C(N2)C(=O)NC(…
PM6 RCSB PDB P80457 152.2 Da LogP 0.64 TPSA 54.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)c(ncn2)S
QUE RCSB PDB P80457 302.2 Da LogP 1.99 TPSA 131.4 ✓ Ro5 Alert c1cc(c(cc1C2=C(C(=O)c3c(cc(cc3O2)O)O)O)O)O
RMO RCSB PDB P80457 251.9 Da LogP -0.48 TPSA 46.5 ✓ Ro5 ✓ Clean O[As]1O[Mo](=O)S1
SAL RCSB PDB P80457 138.1 Da LogP 1.09 TPSA 57.5 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)O)O
TEI RCSB PDB P80457 316.4 Da LogP 3.72 TPSA 83.2 ✓ Ro5 ✓ Clean Cc1c(sc(n1)c2ccc(c(c2)C#N)OCC(C)C)C(=O)O
XAN RCSB PDB P80457 152.1 Da LogP -1.06 TPSA 94.4 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)C(=O)NC(=O)N2
XAX RCSB PDB P80457 554.4 Da LogP -0.03 TPSA 209.1 3 viol. ✓ Clean C([C@@H]1C2=C([C@H]3[C@@H](O1)NC4=C(N3)C(=O)NC(…

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.