Protein profile

PA5421

glutathione-independent formaldehyde dehydrogenase

Genome: NC_002516.2

Gene: PA5421 fdhA Structure source: AlphaFold UniProt Q9HTE3

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Amino acids 399

Annotations 5

Features 17

PDB binders 9

Druggability 0.802

Overview

Basic information about this protein and its source genome.

Accession: PA5421
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA5421 fdhA
Status: annotated
Amino acids: 399
Structure source: AlphaFold

1.2.1.46

GO:0140087 Catalysis of the reaction: acetaldehyde + NAD+ + H2O = acetate + NADH + 2 H+. GO:0018467 Catalysis of the reaction: formaldehyde + H2O + NAD+ = formate + 2 H+ + NADH. GO:0008270 Binding to a zinc ion (Zn). 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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 35.227
Human E-value: 3.65e-06
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

Selected Druggability evidence

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 0.802

Structure –

Pocket –

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)

1.2.1.46

Gene Ontology (GO)

GO:0140087 Catalysis of the reaction: acetaldehyde + NAD+ + H2O = acetate + NADH + 2 H+.
GO:0018467 Catalysis of the reaction: formaldehyde + H2O + NAD+ = formate + 2 H+ + NADH.
GO:0008270 Binding to a zinc ion (Zn).
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.

17 records

Show feature table

Start	End	DB	Term	Name
67	81	ProSitePatterns	PS00059	Zinc-containing alcohol dehydrogenases signature.
67	81	InterPro	IPR002328	Alcohol dehydrogenase, zinc-type, conserved site
172	338	FunFam	G3DSA:3.40.50.720:FF:000166	Glutathione-independent formaldehyde dehydrogenase
4	393	PANTHER	PTHR42813	ZINC-TYPE ALCOHOL DEHYDROGENASE-LIKE
4	392	CDD	cd08282	PFDH_like
183	234	Pfam	PF01262	Alanine dehydrogenase/PNT, C-terminal domain
183	234	InterPro	IPR007698	Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain
4	187	SUPERFAMILY	SSF50129	GroES-like
4	187	InterPro	IPR011032	GroES-like superfamily
7	381	Gene3D	G3DSA:3.90.180.10	-
35	145	Pfam	PF08240	Alcohol dehydrogenase GroES-like domain
35	145	InterPro	IPR013154	Alcohol dehydrogenase-like, N-terminal
2	395	NCBIfam	TIGR02819	formaldehyde dehydrogenase, glutathione-independent
2	395	InterPro	IPR014184	Formaldehyde dehydrogenase, glutathione-independent
177	343	Gene3D	G3DSA:3.40.50.720	-
162	356	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
162	356	InterPro	IPR036291	NAD(P)-binding domain superfamily

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA5421	AlphaFold	—	—	full sequence	—	Viewing

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
3				0.802
11				0.626

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.

64 records

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
BNF	1U3U	P00325	135.2 Da LogP 0.93 TPSA 29.1	✓ Ro5	✓ Clean	`c1ccc(cc1)CNC=O`
BO3	1E3J	O96496	61.8 Da LogP -2.05 TPSA 60.7	✓ Ro5	✓ Clean	`B(O)(O)O`
CAC	3FPL	P14941	137.0 Da LogP -0.52 TPSA 40.1	✓ Ro5	✓ Clean	`C[As](=O)(C)[O-]`
CCB	1U3T	P07327	167.3 Da LogP 1.94 TPSA 20.3	✓ Ro5	✓ Clean	`C1CCC(C1)N(C=O)C2CCC2`
CXL	1HDX	P00325	100.2 Da LogP 1.31 TPSA 20.2	✓ Ro5	✓ Clean	`C1CCC(CC1)O`
FXY	1U3W	P00326	157.3 Da LogP 2.09 TPSA 29.1	✓ Ro5	✓ Clean	`CCCCCC[C@@H](C)NC=O`
HPL	1U3V	P00325	143.2 Da LogP 1.70 TPSA 29.1	✓ Ro5	✓ Clean	`CCCCCCCNC=O`
PYZ	1HSO	P07327	194.0 Da LogP 1.01 TPSA 28.7	✓ Ro5	✓ Clean	`c1c(cn[nH]1)I`
SBT	1BXZ	P14941	74.1 Da LogP 0.78 TPSA 20.2	✓ Ro5	✓ Clean	`CC[C@H](C)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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CND	P07327	8.70	663.4 Da LogP -3.58 TPSA 331.4	3 viol.	✓ Clean	`c1c(c[nH+]cc1C(=O)N)[C@H]2[C@@H]([C@@H]([C@H](O…`
CHEMBL1161866	P07327	6.40	665.4 Da LogP -2.69 TPSA 317.6	3 viol.	✓ Clean	`NC(=O)C1=CN(C2OC(COP(=O)(O)OP(=O)(O)OC[C@H]3O[C…`
CHEMBL48122	P00326	6.39	157.3 Da LogP 2.09 TPSA 29.1	✓ Ro5	✓ Clean	`CCCCCCC(C)NC=O`
CHEMBL45704	P07327	6.06	153.2 Da LogP 1.55 TPSA 20.3	✓ Ro5	✓ Clean	`O=CN(C1CCCC1)C1CC1`
CHEMBL291214	P00325	6.00	141.2 Da LogP 1.31 TPSA 29.1	✓ Ro5	✓ Clean	`O=CNCC1CCCCC1`

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
ZINC1685772	1.000	213.4 Da LogP 3.65 TPSA 29.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC=O`
ZINC5133744	1.000	226.4 Da LogP 4.82 TPSA 20.2	✓ Ro5	✓ Clean	`OC1CCCCCCCCCCCCCC1`
ZINC1599174	0.941	209.3 Da LogP 3.11 TPSA 20.3	✓ Ro5	✓ Clean	`O=CN(C1CCCCC1)C1CCCCC1`
ZINC4795357	0.733	238.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`O[C@@H]1CCCCCC2CCC(CCCC1)CC2`
ZINC4795359	0.733	238.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`O[C@H]1CCCCCC2CCC(CCCC1)CC2`
ZINC12360002	0.681	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703	0.681	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.681	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165	0.681	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC31977053	0.681	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433	0.681	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898	0.681	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.681	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.681	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.681	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022	0.681	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC13518964	0.623	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.623	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.623	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.623	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.623	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.623	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.623	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.623	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.623	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.623	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.623	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.623	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.623	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC31475423	0.622	434.3 Da LogP -2.99 TPSA 238.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@@](=O)(O)OC(=O)…`
ZINC12503850	0.616	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141161066	0.616	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141163786	0.616	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC4228246	0.616	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OS(=O…`
ZINC217396464	0.615	231.3 Da LogP 0.57 TPSA 54.5	✓ Ro5	✓ Clean	`O=CN(C1CCCC1)[C@@H]1CCS(=O)(=O)C1`
ZINC217396539	0.615	231.3 Da LogP 0.57 TPSA 54.5	✓ Ro5	✓ Clean	`O=CN(C1CCCC1)[C@H]1CCS(=O)(=O)C1`
ZINC4096224	0.614	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC105372833	0.600	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC105372837	0.600	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC17107643	0.600	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC204538551	0.600	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC31516918	0.597	446.4 Da LogP -1.33 TPSA 218.2	1 viol.	✓ Clean	`CC(C)[C@H](N)C(=O)O[P@](=O)(O)OC[C@H]1O[C@@H](n…`
ZINC217393737	0.593	245.3 Da LogP 0.96 TPSA 54.5	✓ Ro5	✓ Clean	`O=CN(C1CCCCC1)[C@@H]1CCS(=O)(=O)C1`
ZINC217393810	0.593	245.3 Da LogP 0.96 TPSA 54.5	✓ Ro5	✓ Clean	`O=CN(C1CCCCC1)[C@H]1CCS(=O)(=O)C1`
ZINC6760943	0.591	209.4 Da LogP 3.74 TPSA 12.0	✓ Ro5	✓ Clean	`C1CCC(CNCC2CCCCC2)CC1`
ZINC105469665	0.589	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)CP(=O…`
ZINC3873852	0.589	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873853	0.589	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)CP(=O…`
ZINC3873854	0.589	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873855	0.589	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)CP(=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.