Protein target profile

PA4772

ferredoxin

Genome: NC_002516.2

Gene: PA4772 3D evidence: AlphaFold DB model UniProt Q9HV36

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Length 938

Pocket druggability 0.695

Ligand records 14

EC / GO 1 / 8

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: PA4772
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA4772
Status: annotated
Amino acids: 938
3D evidence: AlphaFold DB model

1.1.2.4

GO:0004458 Catalysis of the reaction: (R)-lactate + 2 [Fe(III)cytochrome c] = 2 [Fe(II)cytochrome c] + 2 H+ + pyruvate. GO:0008720 Catalysis of the reaction: (R)-lactate + NAD+ = H+ + NADH + pyruvate. GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes. GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2. GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms. GO:0046872 Binding to a metal ion.

Target profile

Computed evidence for target prioritization.

Human off-target: Hit
Human identity (%): 27.919
Human E-value: 6.71e-17
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 0.695

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MSLPIPFLETVERLIPRERRFDDPLSTLAFGTDASFYRLIPKLVLRVESEDEVAAILSAAYREQVPVTFRAAGTSLSGQAISDSVLLVLGDNWNGREIRADGAQIRLQPGVIGAQANAWLAPFGRKIGPDPASINACKIGGIVANNASGMCCGTAQNSYHTLAGLRLLLADGTRLDSEDPASVAAFRASHGELLERLAELGRETRANAELAAKIRHKYRLKNTTGLSLNALVDYDEPLDILTHLMVGSEGTLGFISAVTYDTVPEHPHKASALLVFPTVETCCTAVAVLKRQPVSAVELLDRRSLRSVENMQGMPEWVKSLSAGACALLIESRAASRTLLHEQLGRIMASIAEYPLEKQVDFSEDPAVYNQLWRIRKDTFPAVGAVRETGTTVIIEDVTFPVERLAEGVNRLIELFDKHRYDEAILFGHALEGNLHFVFTQGFDSPEQIARYSAFMDDVAHLVAVEYGGSLKAEHGTGRNMAPFVELEWGEDAYRLMWQLKRLLDPRGILNPGVVLSDDPQSHLKNLKPLPAADEIVDKCIECGFCEPVCPSRGLTLTPRQRIVLWRDIQAKKRAGVDTTALERDYRYQGIDTCAATGLCAQRCPVNINTGELIRKLRGADARHAEGATWLARNFAGAMRAARFALLAADGARRLLGAPLLARASRGLSQASGGRVPQWTPALPQPVRLAPPTAPLDDERPRVVYLAACVSRAMGPAFGDEEREPLLDKTRRLLEKAGYQVVFPDNLDNLCCGQPFASKGYAKQADDKRDELLAALLQASRGGLDPIYCDTSPCTLRLVQGLDDPRLQIHDPVKFIRSHLLDRLEFIPQDKPVAVHVTCSTQHLGESQALIDLVGRCTRKVVIPEGIHCCGFAGDKGFTTPELNAHSLRSLKDAVQFCEEGVSTSRTCEIGLSEHGGIDYRGVVYLVDRVTQAKGAPR

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1.1.2.4

Gene Ontology (GO)

GO:0004458 Catalysis of the reaction: (R)-lactate + 2 [Fe(III)cytochrome c] = 2 [Fe(II)cytochrome c] + 2 H+ + pyruvate.
GO:0008720 Catalysis of the reaction: (R)-lactate + NAD+ = H+ + NADH + pyruvate.
GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
GO:0046872 Binding to a metal ion.
GO:1903457 The chemical reactions and pathways resulting in the breakdown of lactate.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

36 records

Show feature table

Start	End	DB	Term	Name
476	515	Gene3D	G3DSA:1.10.45.10	-
476	515	InterPro	IPR016171	Vanillyl-alcohol oxidase, C-terminal subdomain 2
704	795	Pfam	PF02754	Cysteine-rich domain
704	795	InterPro	IPR004017	Cysteine-rich domain
833	893	Pfam	PF02754	Cysteine-rich domain
833	893	InterPro	IPR004017	Cysteine-rich domain
391	475	FunFam	G3DSA:3.30.70.2740:FF:000006	NAD-independent D-lactate dehydrogenase
267	514	Pfam	PF02913	FAD linked oxidases, C-terminal domain
267	514	InterPro	IPR004113	FAD-binding oxidoreductase/transferase, type 4, C-terminal
518	626	FunFam	G3DSA:1.10.1060.10:FF:000019	Oxidoreductase/iron-sulfur cluster-binding protein
529	560	ProSiteProfiles	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
529	560	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
96	265	Gene3D	G3DSA:3.30.465.10	-
96	265	InterPro	IPR016169	FAD-binding, type PCMH, subdomain 2
518	626	Gene3D	G3DSA:1.10.1060.10	-
518	626	InterPro	IPR009051	Alpha-helical ferredoxin
476	516	FunFam	G3DSA:1.10.45.10:FF:000001	D-lactate dehydrogenase mitochondrial
269	521	SUPERFAMILY	SSF55103	FAD-linked oxidases, C-terminal domain
269	521	InterPro	IPR016164	FAD-linked oxidase-like, C-terminal
267	383	Gene3D	G3DSA:3.30.70.2190	-
391	475	Gene3D	G3DSA:3.30.70.2740	-
1	91	FunFam	G3DSA:3.30.43.10:FF:000018	D-lactate dehydrogenase (Dld)
7	264	SUPERFAMILY	SSF56176	FAD-binding/transporter-associated domain-like
7	264	InterPro	IPR036318	FAD-binding, type PCMH-like superfamily
41	175	Pfam	PF01565	FAD binding domain
41	175	InterPro	IPR006094	FAD linked oxidase, N-terminal
492	620	SUPERFAMILY	SSF46548	alpha-helical ferredoxin
540	551	ProSitePatterns	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.
540	551	InterPro	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site
37	265	ProSiteProfiles	PS51387	PCMH-type FAD-binding domain profile.
37	265	InterPro	IPR016166	FAD-binding domain, PCMH-type
9	522	PANTHER	PTHR11748	D-LACTATE DEHYDROGENASE
537	608	Pfam	PF13183	4Fe-4S dicluster domain
537	608	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
2	90	Gene3D	G3DSA:3.30.43.10	-
2	90	InterPro	IPR016167	FAD-binding, type PCMH, subdomain 1

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.

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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 PA4772	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

0.695

Show in viewer

Site 2 FPocket #2

0.53

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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.

14 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 14 via homologs

Structural ligands 5 0 loaded crystals

Bioactive compounds 0 9 ZINC proposed compounds

Drug-like & clean 14 0 PAINS alerts

Best available ligand signal

2HG PDB via homolog 148.1 Da · LogP -0.70 · TPSA 94.8 Open detail RCSB PDB

Detail RCSB PDB 2HG PDB via homolog

Detail RCSB PDB AKG PDB via homolog

Detail RCSB PDB LAC PDB via homolog

Detail RCSB PDB MLT PDB via homolog

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
2HG RCSB PDB	6LPP	Q8N465	148.1 Da LogP -0.70 TPSA 94.8	✓ Ro5	✓ Clean	`C(CC(=O)O)[C@H](C(=O)O)O`
AKG RCSB PDB	6LPX	Q8N465	146.1 Da LogP -0.50 TPSA 91.7	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)C(=O)O`
LAC RCSB PDB	6LPT	Q8N465	90.1 Da LogP -0.55 TPSA 57.5	✓ Ro5	✓ Clean	`C[C@H](C(=O)O)O`
MLT RCSB PDB	6LPQ	Q8N465	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)O)C(=O)O`
S2G RCSB PDB	6LPU	Q8N465	148.1 Da LogP -0.70 TPSA 94.8	✓ Ro5	✓ Clean	`C(CC(=O)O)[C@@H](C(=O)O)O`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC71773889 ZINC	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@H](O)C(=O)O)C[C@H](O)C(=O)O`
ZINC71773890 ZINC	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@H](O)C(=O)O)C[C@@H](O)C(=O)O`
ZINC71773891 ZINC	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@@H](O)C(=O)O)C[C@@H](O)C(=O)O`
ZINC1690029 ZINC	0.571	204.2 Da LogP 0.42 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)CCC(CCC(=O)O)C(=O)O`
ZINC1577651 ZINC	0.526	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O`
ZINC1577652 ZINC	0.526	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O`
ZINC1577653 ZINC	0.526	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](C(=O)O)[C@H](CC(=O)O)C(=O)O`
ZINC220010810 ZINC	0.500	204.2 Da LogP 0.55 TPSA 83.8	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@@H](O)CCC(=O)O`
ZINC238098981 ZINC	0.500	204.2 Da LogP 0.55 TPSA 83.8	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@H](O)CCC(=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.