Protein profile

PA3001

glyceraldehyde-3-phosphate dehydrogenase

Genome: NC_002516.2

Gene: PA3001 Structure source: AlphaFold UniProt Q9HZK4

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Amino acids 461

Annotations 5

Features 27

PDB binders 3

Druggability 0.254

Overview

Basic information about this protein and its source genome.

Accession: PA3001
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA3001
Status: annotated
Amino acids: 461
Structure source: AlphaFold

1.2.1.-

GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH. GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH. GO:0016620 Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP. GO:0006006 The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 41.86
Human E-value: 4.8e-48
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 0.254

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.-

Gene Ontology (GO)

GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
GO:0016620 Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
GO:0006006 The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records

Show feature table

Start	End	DB	Term	Name
266	284	PRINTS	PR00078	Glyceraldehyde-3-phosphate dehydrogenase signature
266	284	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
230	243	PRINTS	PR00078	Glyceraldehyde-3-phosphate dehydrogenase signature
230	243	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
391	406	PRINTS	PR00078	Glyceraldehyde-3-phosphate dehydrogenase signature
391	406	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
293	309	PRINTS	PR00078	Glyceraldehyde-3-phosphate dehydrogenase signature
293	309	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
349	366	PRINTS	PR00078	Glyceraldehyde-3-phosphate dehydrogenase signature
349	366	InterPro	IPR020831	Glyceraldehyde/Erythrose phosphate dehydrogenase family
113	449	Gene3D	G3DSA:3.40.50.720	-
112	222	Pfam	PF00044	Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
112	222	InterPro	IPR020828	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain
1	461	PANTHER	PTHR43454	GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
272	435	SUPERFAMILY	SSF55347	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
270	277	ProSitePatterns	PS00071	Glyceraldehyde 3-phosphate dehydrogenase active site.
270	277	InterPro	IPR020830	Glyceraldehyde 3-phosphate dehydrogenase, active site
111	272	SMART	SM00846	gp_dh_n_7
111	272	InterPro	IPR020828	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain
363	383	Coils	Coil	Coil
113	446	NCBIfam	TIGR01534	glyceraldehyde-3-phosphate dehydrogenase, type I
113	446	InterPro	IPR006424	Glyceraldehyde-3-phosphate dehydrogenase, type I
277	434	Pfam	PF02800	Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
277	434	InterPro	IPR020829	Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain
112	288	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
112	288	InterPro	IPR036291	NAD(P)-binding domain superfamily
271	436	Gene3D	G3DSA:3.30.360.10	Dihydrodipicolinate Reductase; domain 2

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 PA3001	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
2				0.248
1				0.228

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.

54 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
9HB	6LGM	P16858	146.1 Da LogP 0.11 TPSA 52.6	✓ Ro5	✓ Clean	`COC(=O)CCC(=O)OC`
G3H	1NQO	P00362	170.1 Da LogP -1.34 TPSA 104.1	✓ Ro5	✓ Clean	`C([C@H](C=O)O)OP(=O)(O)O`
MLI	6GFP	Q8DIW5	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL63507	P46406	—	336.3 Da LogP -1.72 TPSA 188.2	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CSN=O)C(=O)NCC(=O)O)C(=O…`

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
ZINC3872731	1.000	336.3 Da LogP -1.72 TPSA 188.2	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CSN=O)C(=O)NCC(=O)O)C(=O…`
ZINC3872732	1.000	336.3 Da LogP -1.72 TPSA 188.2	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@H](CSN=O)C(=O)NCC(=O)O)C(=O)O`
ZINC3872733	1.000	336.3 Da LogP -1.72 TPSA 188.2	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)N[C@@H](CSN=O)C(=O)NCC(=O)O)C(=O)O`
ZINC3872734	1.000	336.3 Da LogP -1.72 TPSA 188.2	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)N[C@H](CSN=O)C(=O)NCC(=O)O)C(=O)O`
ZINC1714651	0.813	202.2 Da LogP 0.46 TPSA 69.7	✓ Ro5	✓ Clean	`COC(=O)CCC(=O)CCC(=O)OC`
ZINC1532230	0.750	321.4 Da LogP -1.77 TPSA 158.8	✓ Ro5	✓ Clean	`CSC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC4556979	0.750	321.4 Da LogP -1.77 TPSA 158.8	✓ Ro5	✓ Clean	`CSC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC4556980	0.750	321.4 Da LogP -1.77 TPSA 158.8	✓ Ro5	✓ Clean	`CSC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC4556981	0.750	321.4 Da LogP -1.77 TPSA 158.8	✓ Ro5	✓ Clean	`CSC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC1555765	0.706	244.3 Da LogP 2.84 TPSA 52.6	✓ Ro5	✓ Clean	`COC(=O)CCCCCCCCCC(=O)OC`
ZINC1689486	0.706	216.3 Da LogP 2.06 TPSA 52.6	✓ Ro5	✓ Clean	`COC(=O)CCCCCCCC(=O)OC`
ZINC1699974	0.706	230.3 Da LogP 2.45 TPSA 52.6	✓ Ro5	✓ Clean	`COC(=O)CCCCCCCCC(=O)OC`
ZINC196788889	0.706	205.8 Da LogP 0.14 TPSA 26.3	✓ Ro5	✓ Clean	`COC(=O)CC[Sn+3]`
ZINC2039283	0.706	202.2 Da LogP 1.67 TPSA 52.6	✓ Ro5	✓ Clean	`COC(=O)CCCCCCC(=O)OC`
ZINC4255613	0.706	258.4 Da LogP 3.23 TPSA 52.6	✓ Ro5	✓ Clean	`COC(=O)CCCCCCCCCCC(=O)OC`
ZINC4416389	0.706	286.4 Da LogP 4.01 TPSA 52.6	✓ Ro5	✓ Clean	`COC(=O)CCCCCCCCCCCCC(=O)OC`
ZINC4528570	0.706	272.4 Da LogP 3.62 TPSA 52.6	✓ Ro5	✓ Clean	`COC(=O)CCCCCCCCCCCC(=O)OC`
ZINC5996912	0.706	314.5 Da LogP 4.79 TPSA 52.6	✓ Ro5	✓ Clean	`COC(=O)CCCCCCCCCCCCCCC(=O)OC`
ZINC71404851	0.706	300.4 Da LogP 4.40 TPSA 52.6	✓ Ro5	✓ Clean	`COC(=O)CCCCCCCCCCCCCC(=O)OC`
ZINC13522300	0.702	349.4 Da LogP -1.86 TPSA 175.9	✓ Ro5	✓ Clean	`CC(=O)SC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=…`
ZINC31350707	0.702	349.4 Da LogP -1.86 TPSA 175.9	✓ Ro5	✓ Clean	`CC(=O)SC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC…`
ZINC31350710	0.702	349.4 Da LogP -1.86 TPSA 175.9	✓ Ro5	✓ Clean	`CC(=O)SC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(…`
ZINC31350713	0.702	349.4 Da LogP -1.86 TPSA 175.9	✓ Ro5	✓ Clean	`CC(=O)SC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(…`
ZINC4544082	0.702	335.4 Da LogP -1.38 TPSA 158.8	✓ Ro5	✓ Clean	`CCSC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC4544083	0.702	335.4 Da LogP -1.38 TPSA 158.8	✓ Ro5	✓ Clean	`CCSC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC4544084	0.702	335.4 Da LogP -1.38 TPSA 158.8	✓ Ro5	✓ Clean	`CCSC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC4544085	0.702	335.4 Da LogP -1.38 TPSA 158.8	✓ Ro5	✓ Clean	`CCSC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC13451235	0.688	423.4 Da LogP -2.47 TPSA 233.4	1 viol.	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CS[C@H](CC(=O)O)C(=O)O)C…`
ZINC145953214	0.688	365.4 Da LogP -2.02 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](O)CSC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O…`
ZINC145953600	0.688	365.4 Da LogP -2.02 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](O)CSC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)…`
ZINC14966489	0.688	423.4 Da LogP -2.47 TPSA 233.4	1 viol.	✓ Clean	`N[C@H](CCC(=O)N[C@@H](CS[C@@H](CC(=O)O)C(=O)O)C…`
ZINC14966492	0.688	423.4 Da LogP -2.47 TPSA 233.4	1 viol.	✓ Clean	`N[C@H](CCC(=O)N[C@H](CS[C@@H](CC(=O)O)C(=O)O)C(…`
ZINC201224060	0.688	365.4 Da LogP -2.02 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](O)CSC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)…`
ZINC253638410	0.688	423.4 Da LogP -2.47 TPSA 233.4	1 viol.	✓ Clean	`N[C@H](CCC(=O)N[C@H](CS[C@H](CC(=O)O)C(=O)O)C(=…`
ZINC253638411	0.688	423.4 Da LogP -2.47 TPSA 233.4	1 viol.	✓ Clean	`N[C@H](CCC(=O)N[C@@H](CS[C@H](CC(=O)O)C(=O)O)C(…`
ZINC3920510	0.688	423.4 Da LogP -2.47 TPSA 233.4	1 viol.	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CS[C@@H](CC(=O)O)C(=O)O)…`
ZINC77300920	0.688	365.4 Da LogP -2.02 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](O)CSC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)N…`
ZINC3870222	0.673	379.4 Da LogP -2.50 TPSA 196.1	1 viol.	✓ Clean	`C[C@H](O)C(=O)SC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(…`
ZINC4556756	0.673	377.4 Da LogP -2.29 TPSA 193.0	✓ Ro5	✓ Clean	`CC(=O)C(=O)SC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)…`
ZINC4556757	0.673	377.4 Da LogP -2.29 TPSA 193.0	✓ Ro5	✓ Clean	`CC(=O)C(=O)SC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O…`
ZINC4556758	0.673	377.4 Da LogP -2.29 TPSA 193.0	✓ Ro5	✓ Clean	`CC(=O)C(=O)SC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O…`
ZINC4556759	0.673	377.4 Da LogP -2.29 TPSA 193.0	✓ Ro5	✓ Clean	`CC(=O)C(=O)SC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=…`
ZINC4962281	0.673	349.4 Da LogP -0.99 TPSA 158.8	✓ Ro5	✓ Clean	`CCCSC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC504173140	0.673	365.4 Da LogP -2.02 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](CO)SC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)…`
ZINC504173141	0.673	365.4 Da LogP -2.02 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](CO)SC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)…`
ZINC504173142	0.673	365.4 Da LogP -2.02 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](CO)SC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O…`
ZINC5883749	0.673	364.4 Da LogP -2.06 TPSA 187.9	1 viol.	✓ Clean	`CNC(=O)SC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(…`
ZINC5883754	0.673	364.4 Da LogP -2.06 TPSA 187.9	1 viol.	✓ Clean	`CNC(=O)SC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC…`
ZINC5883758	0.673	364.4 Da LogP -2.06 TPSA 187.9	1 viol.	✓ Clean	`CNC(=O)SC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NC…`
ZINC77300937	0.673	365.4 Da LogP -2.02 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](CO)SC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)N…`

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.