Protein profile

PA5046

malic enzyme

Genome: NC_002516.2

Gene: PA5046 Structure source: AlphaFold UniProt Q9HUD3

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Amino acids 422

Annotations 6

Features 24

PDB binders 13

Druggability 0.566

Overview

Basic information about this protein and its source genome.

Accession: PA5046
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA5046
Status: annotated
Amino acids: 422
Structure source: AlphaFold

1.1.1.40

GO:0004473 Catalysis of the reaction: (S)-malate + NADP+ = pyruvate + CO2 + NADPH. GO:0046872 Binding to a metal ion. 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:0004470 Catalysis of the oxidative decarboxylation of malate with the concomitant production of pyruvate. GO:0004471 Catalysis of the reaction: (S)-malate + NAD+ = pyruvate + CO2 + NADH.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 30.435
Human E-value: 6.49e-11
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 0.566

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1.1.1.40

Gene Ontology (GO)

GO:0004473 Catalysis of the reaction: (S)-malate + NADP+ = pyruvate + CO2 + NADPH.
GO:0046872 Binding to a metal ion.
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:0004470 Catalysis of the oxidative decarboxylation of malate with the concomitant production of pyruvate.
GO:0004471 Catalysis of the reaction: (S)-malate + NAD+ = pyruvate + CO2 + NADH.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records

Show feature table

Start	End	DB	Term	Name
160	420	FunFam	G3DSA:3.40.50.720:FF:000095	NADP-dependent malic enzyme
162	397	CDD	cd05311	NAD_bind_2_malic_enz
162	397	InterPro	IPR045213	Malic enzyme, NAD-binding domain, bacterial type
2	409	PANTHER	PTHR43237	NADP-DEPENDENT MALIC ENZYME
164	354	Pfam	PF03949	Malic enzyme, NAD binding domain
164	354	InterPro	IPR012302	Malic enzyme, NAD-binding
158	174	ProSitePatterns	PS00331	Malic enzymes signature.
158	174	InterPro	IPR015884	Malic enzyme, conserved site
19	148	Pfam	PF00390	Malic enzyme, N-terminal domain
19	148	InterPro	IPR012301	Malic enzyme, N-terminal domain
162	398	SMART	SM00919	Malic_M_2
162	398	InterPro	IPR012302	Malic enzyme, NAD-binding
160	418	Gene3D	G3DSA:3.40.50.720	-
9	160	SUPERFAMILY	SSF53223	Aminoacid dehydrogenase-like, N-terminal domain
9	160	InterPro	IPR046346	Aminoacid dehydrogenase-like, N-terminal domain superfamily
1	159	FunFam	G3DSA:3.40.50.10380:FF:000003	NADP-dependent malic enzyme
17	150	SMART	SM01274	malic_2
17	150	InterPro	IPR012301	Malic enzyme, N-terminal domain
44	418	PIRSF	PIRSF000106	ME
44	418	InterPro	IPR001891	Malic oxidoreductase
1	159	Gene3D	G3DSA:3.40.50.10380	-
1	159	InterPro	IPR037062	Malic enzyme, N-terminal domain superfamily
162	412	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
162	412	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 PA5046	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				0.566

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.

65 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
FUM	1GZ3	P23368	116.1 Da LogP -0.29 TPSA 74.6	✓ Ro5	✓ Clean	`C(=C/C(=O)O)\C(=O)O`
MAK	1EFK	P23368	118.0 Da LogP -1.28 TPSA 91.7	✓ Ro5	✓ Clean	`C(=O)(C(=O)O)C(=O)O`
MLT	1PJ4	P23368	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)O)C(=O)O`
OXL	1DO8	P23368	88.0 Da LogP -3.51 TPSA 80.3	✓ Ro5	✓ Clean	`C(=O)(C(=O)[O-])[O-]`
PYR	1PJ3	P23368	88.1 Da LogP -0.34 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)C(=O)O`
SEV	6W29	Q4DJ68	418.4 Da LogP 4.03 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(cc1)NS(=O)(=O)c2cccc(c2)NC(=O)c3cc(cc(c…`
SJD	6W2N	Q4DJ68	436.4 Da LogP 4.17 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(c(c1)F)NS(=O)(=O)c2cccc(c2)NC(=O)c3cc(c…`
SWV	6W49	Q4DJ68	372.4 Da LogP 2.67 TPSA 101.1	✓ Ro5	✓ Clean	`c1ccc(c(c1)NS(=O)(=O)c2cccc(c2)NC(=O)c3cnccn3)F`
SZD	6W59	Q4DJ68	472.4 Da LogP 4.92 TPSA 84.5	✓ Ro5	✓ Clean	`c1cc(cc(c1)S(=O)(=O)Nc2ccc(cc2)OC(F)(F)F)NC(=O)…`
SZG	6W57	Q4DJ68	488.8 Da LogP 5.27 TPSA 84.5	1 viol.	✓ Clean	`c1cc(ccc1NS(=O)(=O)c2ccc(c(c2)NC(=O)c3cc(cc(c3)…`
SZJ	6W56	Q4DJ68	454.4 Da LogP 4.62 TPSA 84.5	✓ Ro5	✓ Clean	`c1cc(cc(c1)S(=O)(=O)Nc2ccc(cc2)OC(F)F)NC(=O)c3c…`
SZP	6W53	Q4DJ68	506.8 Da LogP 5.57 TPSA 84.5	2 viol.	✓ Clean	`c1cc(ccc1NS(=O)(=O)c2ccc(c(c2)NC(=O)c3cc(cc(c3)…`
TTN	1O0S	P27443	118.0 Da LogP -4.15 TPSA 100.5	✓ Ro5	✓ Clean	`C(C(=O)[O-])(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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
G9A	Q16798	—	130.1 Da LogP 0.10 TPSA 74.6	✓ Ro5	✓ Clean	`C(/C=C/C(=O)O)C(=O)O`
MAE	Q16798	—	116.1 Da LogP -0.29 TPSA 74.6	✓ Ro5	✓ Clean	`C(=C/C(=O)O)/C(=O)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
ZINC8289540	0.809	412.5 Da LogP 3.76 TPSA 93.7	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccc(OC)cc3)c2)…`
ZINC9217064	0.792	388.8 Da LogP 3.18 TPSA 101.0	✓ Ro5	✓ Clean	`O=C(Nc1cccc(S(=O)(=O)Nc2ccccc2Cl)c1)c1cnccn1`
ZINC8287843	0.784	400.4 Da LogP 3.89 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(C(=O)Nc3cccc(F)c3)c2)c…`
ZINC5864247	0.776	382.4 Da LogP 3.75 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccccc3)c2)cc1`
ZINC8289545	0.760	412.5 Da LogP 3.76 TPSA 93.7	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3cccc(OC)c3)c2)…`
ZINC12532621	0.759	466.4 Da LogP 4.65 TPSA 93.7	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccc(OC(F)(F)F)…`
ZINC12552275	0.745	418.4 Da LogP 4.03 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccccc1NS(=O)(=O)c1cccc(NC(=O)c2cc(F)cc(F)c2…`
ZINC68732608	0.745	400.4 Da LogP 3.89 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)c2ccc(NS(=O)(=O)c3cccc(F)c3)cc2)c…`
ZINC89444372	0.745	400.4 Da LogP 3.89 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)c2cccc(S(=O)(=O)Nc3ccc(F)cc3)c2)c…`
ZINC9715810	0.736	450.4 Da LogP 4.77 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccc(C(F)(F)F)c…`
ZINC5557605	0.725	415.4 Da LogP 4.28 TPSA 96.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)Nc3ccc(F)cc3)c2)…`
ZINC10027204	0.722	388.8 Da LogP 3.18 TPSA 101.0	✓ Ro5	✓ Clean	`O=C(Nc1cccc(S(=O)(=O)Nc2ccc(Cl)cc2)c1)c1cnccn1`
ZINC8129611	0.717	371.4 Da LogP 3.27 TPSA 88.2	✓ Ro5	✓ Clean	`O=C(Nc1cccc(S(=O)(=O)Nc2ccccc2F)c1)c1ccncc1`
ZINC3014061	0.714	412.5 Da LogP 3.76 TPSA 93.7	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)c2cccc(S(=O)(=O)Nc3ccc(OC)cc3)c2)…`
ZINC823266	0.706	382.4 Da LogP 3.75 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(C(=O)Nc3ccccc3)c2)cc1`
ZINC6046379	0.702	400.4 Da LogP 3.89 TPSA 84.5	✓ Ro5	✓ Clean	`COc1cccc(C(=O)Nc2cccc(S(=O)(=O)Nc3ccccc3F)c2)c1`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC754833	0.698	426.5 Da LogP 3.45 TPSA 121.8	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(C(=O)Nc3cccc(C(=O)O)c3…`
ZINC89651324	0.698	432.4 Da LogP 4.33 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cc(NC(=O)c3cc(F)cc(F)c3)ccc…`
ZINC1104233	0.679	400.4 Da LogP 3.89 TPSA 84.5	✓ Ro5	✓ Clean	`COc1cccc(S(=O)(=O)Nc2ccc(C(=O)Nc3ccc(F)cc3)cc2)…`
ZINC12507851	0.679	422.5 Da LogP 4.24 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccc4c(c3)CCC4)…`
ZINC12556970	0.679	448.4 Da LogP 4.35 TPSA 93.7	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(C(=O)Nc3ccc(OC(F)F)cc3…`
ZINC27496348	0.673	414.5 Da LogP 3.82 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)Cc3ccc(F)cc3)c2)…`
ZINC12541977	0.667	447.5 Da LogP 4.54 TPSA 89.4	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3cccc(-n4cccc4)…`
ZINC5652634	0.667	388.5 Da LogP 3.81 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3cccs3)c2)cc1`
ZINC6244639	0.667	371.4 Da LogP 3.27 TPSA 88.2	✓ Ro5	✓ Clean	`O=C(Nc1cccnc1)c1cccc(S(=O)(=O)Nc2ccccc2F)c1`
ZINC6510588	0.667	317.2 Da LogP 4.12 TPSA 38.3	✓ Ro5	✓ Clean	`O=C(Nc1ccc(OC(F)(F)F)cc1)c1cc(F)cc(F)c1`
ZINC71773889	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	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	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`
ZINC9612539	0.667	417.9 Da LogP 3.80 TPSA 97.4	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccc(Cl)nc3)c2)…`
ZINC21875823	0.660	418.4 Da LogP 4.34 TPSA 84.5	✓ Ro5	✓ Clean	`O=C(Nc1ccc(OC(F)F)cc1)c1ccc(NS(=O)(=O)c2ccccc2)…`
ZINC21877086	0.660	436.4 Da LogP 4.64 TPSA 84.5	✓ Ro5	✓ Clean	`O=C(Nc1ccc(OC(F)(F)F)cc1)c1ccc(NS(=O)(=O)c2cccc…`
ZINC3329693	0.660	341.3 Da LogP 3.29 TPSA 72.5	✓ Ro5	✓ Clean	`CC(=O)c1cccc(S(=O)(=O)Nc2ccc(OC(F)F)cc2)c1`
ZINC7055979	0.660	359.3 Da LogP 3.59 TPSA 72.5	✓ Ro5	✓ Clean	`CC(=O)c1cccc(S(=O)(=O)Nc2ccc(OC(F)(F)F)cc2)c1`
ZINC7055973	0.660	335.3 Da LogP 3.53 TPSA 55.4	✓ Ro5	✓ Clean	`O=S(=O)(Nc1ccc(OC(F)(F)F)cc1)c1cccc(F)c1`
ZINC7409087	0.660	317.3 Da LogP 3.23 TPSA 55.4	✓ Ro5	✓ Clean	`O=S(=O)(Nc1ccc(OC(F)F)cc1)c1cccc(F)c1`
ZINC12739009	0.655	375.4 Da LogP 3.18 TPSA 101.3	✓ Ro5	✓ Clean	`Cc1cc(C(=O)Nc2cccc(S(=O)(=O)Nc3ccccc3F)c2)no1`
ZINC89453684	0.655	456.5 Da LogP 4.24 TPSA 101.6	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)CCC(=O)c3ccc(F)c…`
ZINC9217066	0.655	426.5 Da LogP 3.48 TPSA 103.0	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccc4c(c3)OCO4)…`
ZINC9514424	0.655	491.5 Da LogP 4.59 TPSA 126.7	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccc(NC(=O)c4cc…`
ZINC5881828	0.655	383.4 Da LogP 3.14 TPSA 97.4	✓ Ro5	✓ Clean	`COc1ccc(NS(=O)(=O)c2cccc(NC(=O)c3ccccn3)c2)cc1`
ZINC6046622	0.655	416.9 Da LogP 4.40 TPSA 84.5	✓ Ro5	✓ Clean	`COc1cccc(C(=O)Nc2cccc(S(=O)(=O)Nc3ccc(Cl)cc3)c2…`
ZINC2635861	0.654	361.3 Da LogP 3.08 TPSA 92.7	✓ Ro5	✓ Clean	`O=C(O)c1cccc(S(=O)(=O)Nc2ccc(OC(F)(F)F)cc2)c1`
ZINC3452732	0.652	263.2 Da LogP 3.23 TPSA 38.3	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)c2cc(F)cc(F)c2)cc1`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC3154686	0.648	426.5 Da LogP 3.45 TPSA 121.8	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)c2cccc(S(=O)(=O)Nc3ccc(C(=O)O)cc3…`
ZINC89444368	0.648	416.9 Da LogP 4.40 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)c2cccc(S(=O)(=O)Nc3ccc(Cl)cc3)c2)…`

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.