Protein profile

PA3418

leucine dehydrogenase

Genome: NC_002516.2

Gene: PA3418 ldh Structure source: Experimental + AlphaFold UniProt Q9HYI7

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Amino acids 341

Annotations 4

Features 23

PDB binders 9

Druggability 0.606

Overview

Basic information about this protein and its source genome.

Accession: PA3418
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA3418 ldh
Status: annotated
Amino acids: 341
Structure source: Experimental + AlphaFold

GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. GO:0016639 Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP. GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups. 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 (%): 26.059
Human E-value: 6.33e-09
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 0.606

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
GO:0016639 Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
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.

23 records

Show feature table

Start	End	DB	Term	Name
140	338	CDD	cd01075	NAD_bind_Leu_Phe_Val_DH
2	336	Gene3D	G3DSA:3.40.50.10860	Leucine Dehydrogenase, chain A, domain 1
138	339	SMART	SM00839	ELFV_dehydrog_3
138	339	InterPro	IPR006096	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, C-terminal
22	129	Pfam	PF02812	Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
22	129	InterPro	IPR006097	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, dimerisation domain
2	134	SUPERFAMILY	SSF53223	Aminoacid dehydrogenase-like, N-terminal domain
2	134	InterPro	IPR046346	Aminoacid dehydrogenase-like, N-terminal domain superfamily
214	290	Pfam	PF00208	Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
214	290	InterPro	IPR006096	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, C-terminal
132	330	Gene3D	G3DSA:3.40.50.720	-
138	335	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
138	335	InterPro	IPR036291	NAD(P)-binding domain superfamily
64	78	PRINTS	PR00082	Glutamate/leucine/phenylalanine/valine dehydrogenase signature
64	78	InterPro	IPR006095	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase
280	291	PRINTS	PR00082	Glutamate/leucine/phenylalanine/valine dehydrogenase signature
280	291	InterPro	IPR006095	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase
170	190	PRINTS	PR00082	Glutamate/leucine/phenylalanine/valine dehydrogenase signature
170	190	InterPro	IPR006095	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase
2	337	PANTHER	PTHR42722	LEUCINE DEHYDROGENASE
2	337	InterPro	IPR016211	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, bacterial/archaeal
1	341	PIRSF	PIRSF000188	Phe_leu_dh
1	341	InterPro	IPR016211	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, bacterial/archaeal

3D Structure

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

Loading 3D structure...

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Structural evidence

1 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 7VID	X-ray	2.50 Å	A,B	100.0% 1-341	PDBe RCSB PDBj File	Viewing
AlphaFold PA3418	AlphaFold	—	—	full sequence	—	Loaded

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				0.606
3				0.551
1				0.437

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				24.55	0.899

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
1				0.697
3				0.438

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.

61 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
AKG	1HWY	P00366	146.1 Da LogP -0.50 TPSA 91.7	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)C(=O)O`
B1T	3ETD	P00366	356.1 Da LogP 5.86 TPSA 40.5	1 viol.	✓ Clean	`c1c(cc(c(c1Sc2cc(cc(c2O)Cl)Cl)O)Cl)Cl`
GWD	3ETG	P00366	520.9 Da LogP 5.01 TPSA 49.3	2 viol.	✓ Clean	`c1cc2c(cc1I)/C(=C\c3cc(c(c(c3)Br)O)Br)/C(=O)N2`
H3P	3ETE	P00366	406.9 Da LogP 6.61 TPSA 40.5	1 viol.	✓ Clean	`c1c(c(c(c(c1Cl)Cl)Cc2c(c(cc(c2Cl)Cl)Cl)O)O)Cl`
HCI	1BXG	Q59771	150.2 Da LogP 1.70 TPSA 37.3	✓ Ro5	✓ Clean	`c1ccc(cc1)CCC(=O)O`
HFA	1C1X	Q59771	166.2 Da LogP 0.67 TPSA 57.5	✓ Ro5	✓ Clean	`c1ccc(cc1)C[C@@H](C(=O)O)O`
NH4	3AOG	Q72IC1	18.0 Da LogP 0.38 TPSA 36.5	✓ Ro5	✓ Clean	`[NH4+]`
PPY	1BW9	Q59771	164.2 Da LogP 0.88 TPSA 54.4	✓ Ro5	✓ Clean	`c1ccc(cc1)CC(=O)C(=O)O`
XEG	6DHL	P00366	442.4 Da LogP 2.53 TPSA 177.1	1 viol.	Alert	`c1cc(c(cc1[C@@H]2[C@H](Cc3c(cc(cc3O2)O)O)OC(=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
CHEMBL3400559	P00366	—	817.5 Da LogP 1.07 TPSA 345.0	3 viol.	✓ Clean	`C/C(=C\c1ccc(C2(C(F)(F)F)N=N2)cc1O)C(=O)NCCNP(=…`
CHEMBL3400560	P00366	—	737.5 Da LogP 0.96 TPSA 298.5	3 viol.	✓ Clean	`C/C(=C\c1ccc(C2(C(F)(F)F)N=N2)cc1O)C(=O)NCCNP(=…`

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
ZINC3978503	1.000	442.4 Da LogP 2.53 TPSA 177.1	1 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1ccc(O)c(O)…`
ZINC4534390	1.000	442.4 Da LogP 2.53 TPSA 177.1	1 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1ccc(O)c(O)c…`
ZINC4544252	1.000	442.4 Da LogP 2.53 TPSA 177.1	1 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@H]1c1ccc(O)c(O)c1…`
ZINC8681494	1.000	442.4 Da LogP 2.53 TPSA 177.1	1 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@H]1c1ccc(O)c(O)c…`
ZINC3870412	0.851	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1cc(O)c(O)c…`
ZINC3870413	0.851	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@H]1c1cc(O)c(O)c(…`
ZINC3870414	0.851	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1cc(O)c(O)c(…`
ZINC3870415	0.851	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@H]1c1cc(O)c(O)c(O…`
ZINC14642643	0.849	456.4 Da LogP 2.83 TPSA 166.1	1 viol.	Alert	`COc1cc(C(=O)O[C@@H]2Cc3c(O)cc(O)cc3O[C@@H]2c2cc…`
ZINC14727965	0.837	426.4 Da LogP 2.82 TPSA 156.9	1 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1ccc(O)cc1)…`
ZINC1602735	0.800	238.3 Da LogP 2.61 TPSA 34.1	✓ Ro5	Alert	`O=C(Cc1ccccc1)C(=O)Cc1ccccc1`
ZINC406914	0.800	222.2 Da LogP 1.72 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCc1ccc(CCC(=O)O)cc1`
ZINC2244337	0.778	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(-c2ccccc2)cc1)C(=O)O`
ZINC2244338	0.778	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(-c2ccccc2)cc1)C(=O)O`
ZINC3843497	0.762	370.0 Da LogP 4.71 TPSA 80.9	✓ Ro5	✓ Clean	`Oc1c(Cl)cc(Cl)c(O)c1Cc1c(O)c(Cl)cc(Cl)c1O`
ZINC22219569	0.750	240.3 Da LogP 2.55 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)C(=O)Cc1ccc(-c2ccccc2)cc1`
ZINC9998612	0.750	226.3 Da LogP 3.37 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCc1ccc(-c2ccccc2)cc1`
ZINC14436185	0.741	472.4 Da LogP 2.54 TPSA 186.4	2 viol.	Alert	`COc1cc(C(=O)O[C@@H]2Cc3c(O)cc(O)cc3O[C@@H]2c2cc…`
ZINC2163727	0.739	222.2 Da LogP 1.72 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCc1cccc(CCC(=O)O)c1`
ZINC1673354	0.727	238.3 Da LogP 3.82 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(CCc1ccccc1)CCc1ccccc1`
ZINC1693912	0.727	266.3 Da LogP 3.39 TPSA 34.1	✓ Ro5	Alert	`O=C(CCc1ccccc1)C(=O)CCc1ccccc1`
ZINC2561081	0.724	269.3 Da LogP 1.87 TPSA 80.4	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(C(=O)c2ccccc2)cc1)C(=O)O`
ZINC2561082	0.724	269.3 Da LogP 1.87 TPSA 80.4	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(C(=O)c2ccccc2)cc1)C(=O)O`
ZINC21992193	0.722	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1cc(O)c(O)c…`
ZINC21992196	0.722	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1cc(O)c(O)c(…`
ZINC21992198	0.722	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@H]1c1cc(O)c(O)c(…`
ZINC21992201	0.722	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@H]1c1cc(O)c(O)c(O…`
ZINC29566843	0.700	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1cccc(-c2ccccc2)c1)C(=O)O`
ZINC29570997	0.700	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1cccc(-c2ccccc2)c1)C(=O)O`
ZINC247409588	0.692	220.3 Da LogP 2.44 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)CCc1ccccc1`
ZINC1616445	0.690	354.5 Da LogP 0.36 TPSA 110.2	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1)C(=O)NCCNC(=O)[C@H](N)Cc1cccc…`
ZINC1616446	0.690	354.5 Da LogP 0.36 TPSA 110.2	✓ Ro5	✓ Clean	`N[C@H](Cc1ccccc1)C(=O)NCCNC(=O)[C@H](N)Cc1ccccc1`
ZINC1616447	0.690	354.5 Da LogP 0.36 TPSA 110.2	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1)C(=O)NCCNC(=O)[C@@H](N)Cc1ccc…`
ZINC1903857763	0.689	411.0 Da LogP 4.12 TPSA 69.6	✓ Ro5	Alert	`O=C1Nc2ccc(Br)cc2C1=Cc1cc(O)c(O)c(Br)c1`
ZINC2104376	0.689	411.0 Da LogP 4.12 TPSA 69.6	✓ Ro5	Alert	`O=C1Nc2ccc(Br)cc2/C1=C/c1cc(O)c(O)c(Br)c1`
ZINC96481959	0.689	411.0 Da LogP 4.12 TPSA 69.6	✓ Ro5	Alert	`O=C1Nc2ccc(Br)cc2/C1=C\c1cc(O)c(O)c(Br)c1`
ZINC133159	0.688	271.3 Da LogP 2.22 TPSA 72.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(OCc2ccccc2)cc1)C(=O)O`
ZINC133162	0.688	271.3 Da LogP 2.22 TPSA 72.5	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(OCc2ccccc2)cc1)C(=O)O`
ZINC1558609	0.680	248.4 Da LogP 4.43 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCc1ccccc1`
ZINC2510086	0.680	262.4 Da LogP 4.82 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCc1ccccc1`
ZINC2575483	0.680	206.3 Da LogP 3.26 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCc1ccccc1`
ZINC2575484	0.680	220.3 Da LogP 3.65 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCc1ccccc1`
ZINC2575485	0.680	234.3 Da LogP 4.04 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCc1ccccc1`
ZINC6580731	0.679	225.3 Da LogP 2.44 TPSA 43.1	✓ Ro5	✓ Clean	`N[C@H](Cc1ccccc1)C(=O)c1ccccc1`
ZINC90624143	0.679	225.3 Da LogP 2.44 TPSA 43.1	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1)C(=O)c1ccccc1`
ZINC12648454	0.677	272.3 Da LogP 2.25 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)[C@@H](O)Cc1ccc(OCc2ccccc2)cc1`
ZINC32098866	0.677	272.3 Da LogP 2.25 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)[C@H](O)Cc1ccc(OCc2ccccc2)cc1`
ZINC11962728	0.667	242.3 Da LogP 3.50 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)CCc1ccc(Oc2ccccc2)cc1`
ZINC32101929	0.667	245.1 Da LogP 1.44 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)[C@H](O)Cc1ccc(Br)cc1`
ZINC84379438	0.667	292.1 Da LogP 1.28 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)[C@H](O)Cc1ccc(I)cc1`

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.