Protein profile

PA3570

methylmalonate-semialdehyde dehydrogenase

Genome: NC_002516.2

Gene: PA3570 mmsA Structure source: AlphaFold UniProt P28810

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Amino acids 497

Annotations 6

Features 18

PDB binders 8

Druggability 0.69

Overview

Basic information about this protein and its source genome.

Accession: PA3570
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA3570 mmsA
Status: annotated
Amino acids: 497
Structure source: AlphaFold

1.2.1.27

GO:0004491 Catalysis of the reaction: 2-methyl-3-oxopropanoate + CoA + NAD+ = propanoyl-CoA + hydrogencarbonate + NADH + H+. Can also use malonate (3-oxopropanoate) as a substrate. The reaction occurs in two steps with the decarboxylation process preceding CoA-binding. Bicarbonate rather than CO2 is released as a final product. GO:0006574 The chemical reactions and pathways resulting in the breakdown of L-valine. GO:0006210 The chemical reactions and pathways resulting in the breakdown of thymine, 5-methyluracil, one of the two major pyrimidine bases present (as thymidine) in DNA but not found in RNA other than (as ribothymidine) in transfer RNA, where it is a minor base. 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: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 (%): 55.462
Human E-value: 3.64e-100
Gut microbiome off-target: hit
Essential (DEG): N
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 0.69

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MSVPVRHLIAGAFVEGLGAQRIPVSNPLDNSTLAEIACASAEQVEQAVASARETFASWKETPVSERARVMLRYQALLKEHHDELAKIVSSELGKTFEDAKGDVWRGIEVVEHACNVPSLLMGETVENVARNIDTYSITQPLGVCVGITPFNFPAMIPLWMFPLAIACGNAFILKPSEQVPLTSVRLAELFLEAGAPKGVLQVVHGGKEQVDQLLKHPQVKAVSFVGSVAVGQYVYHTGTAHNKRVQSFAGAKNHMVIMPDADKAQVISNLVGASVGAAGQRCMAISVAVLVGAAREWIPEIRDALAKVRPGPWDDSGASYGPVINPQAKARIERLIGQGVEEGAQLLLDGRGYKVEGYPDGNWVGPTLFAGVRPDMAIYREEVFGPVLCLAEVDSLEQAIRLINESPYGNGTSIFTSSGAAARTFQHHIEVGQVGINIPIPVPLPFFSFTGWKGSFYGDLHAYGKQGVRFYTETKTVTARWFDSDSVAGTNFSIQMR

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1.2.1.27

Gene Ontology (GO)

GO:0004491 Catalysis of the reaction: 2-methyl-3-oxopropanoate + CoA + NAD+ = propanoyl-CoA + hydrogencarbonate + NADH + H+. Can also use malonate (3-oxopropanoate) as a substrate. The reaction occurs in two steps with the decarboxylation process preceding CoA-binding. Bicarbonate rather than CO2 is released as a final product.
GO:0006574 The chemical reactions and pathways resulting in the breakdown of L-valine.
GO:0006210 The chemical reactions and pathways resulting in the breakdown of thymine, 5-methyluracil, one of the two major pyrimidine bases present (as thymidine) in DNA but not found in RNA other than (as ribothymidine) in transfer RNA, where it is a minor base.
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: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.

18 records

Show feature table

Start	End	DB	Term	Name
4	494	PANTHER	PTHR43866	MALONATE-SEMIALDEHYDE DEHYDROGENASE
4	494	InterPro	IPR010061	Methylmalonate-semialdehyde dehydrogenase
5	481	NCBIfam	TIGR01722	CoA-acylating methylmalonate-semialdehyde dehydrogenase
5	481	InterPro	IPR010061	Methylmalonate-semialdehyde dehydrogenase
5	481	CDD	cd07085	ALDH_F6_MMSDH
9	256	FunFam	G3DSA:3.40.605.10:FF:000003	Methylmalonate-semialdehyde dehydrogenase [acylating]
18	477	Pfam	PF00171	Aldehyde dehydrogenase family
18	477	InterPro	IPR015590	Aldehyde dehydrogenase domain
41	61	Coils	Coil	Coil
250	450	Gene3D	G3DSA:3.40.309.10	Aldehyde Dehydrogenase; Chain A, domain 2
250	450	InterPro	IPR016163	Aldehyde dehydrogenase, C-terminal
250	450	FunFam	G3DSA:3.40.309.10:FF:000002	Methylmalonate-semialdehyde dehydrogenase (Acylating)
3	483	SUPERFAMILY	SSF53720	ALDH-like
3	483	InterPro	IPR016161	Aldehyde/histidinol dehydrogenase
275	286	ProSitePatterns	PS00070	Aldehyde dehydrogenases cysteine active site.
275	286	InterPro	IPR016160	Aldehyde dehydrogenase, cysteine active site
25	458	Gene3D	G3DSA:3.40.605.10	Aldehyde Dehydrogenase; Chain A, domain 1
25	458	InterPro	IPR016162	Aldehyde dehydrogenase, N-terminal

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

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 PA3570	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
1				0.69
2				0.333

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
7PE	2WOX	Q9HTJ1	310.4 Da LogP 0.10 TPSA 75.6	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCO`
DTT	4CBB	Q9HTJ1	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@@H]([C@H](CS)O)O)S`
DXC	2OPX	P25553	392.6 Da LogP 4.48 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)O)[C@H]1CC[C@@H]2[C@@]1([C@H](C[C…`
LAC	2IMP	P25553	90.1 Da LogP -0.55 TPSA 57.5	✓ Ro5	✓ Clean	`C[C@H](C(=O)O)O`
PE4	4CAZ	Q9HTJ1	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
SIN	6WSA	Q3JLL8	118.1 Da LogP -0.06 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)O`
TOE	2XDR	Q9HTJ1	164.2 Da LogP -0.34 TPSA 47.9	✓ Ro5	✓ Clean	`COCCOCCOCCO`
TXE	4CAZ	Q9HTJ1	667.5 Da LogP -2.95 TPSA 317.6	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`

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
CHEMBL449188	P13601	6.80	686.6 Da LogP -0.01 TPSA 262.7	3 viol.	Alert	`O=C1c2cc(CO)cc(O)c2C(=O)c2c1ccc(C1(C3O[C@H](CO)…`
CHEMBL494494	P13601	6.28	723.1 Da LogP 0.41 TPSA 262.7	3 viol.	Alert	`Cl.O=C1c2cc(CO)cc(O)c2C(=O)c2c1ccc(C1(C3O[C@H](…`
CHEMBL5169766	P49189	—	298.4 Da LogP 2.55 TPSA 69.0	✓ Ro5	✓ Clean	`N#CN1CC[C@H](C(=O)Nc2ncc(-c3ccccc3)s2)C1`

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
ZINC12493596	1.000	392.6 Da LogP 4.48 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)O)[C@H]1CC[C@H]2[C@@H]3CC[C@H]4C[…`
ZINC1580161	1.000	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	1.000	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	1.000	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC257356883	1.000	392.6 Da LogP 4.48 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)O)[C@@H]1CC[C@@H]2[C@@H]3CC[C@H]4…`
ZINC257356885	1.000	392.6 Da LogP 4.48 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)O)[C@@H]1CC[C@@H]2[C@@H]3CC[C@H]4…`
ZINC34317654	1.000	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	1.000	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	1.000	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743	1.000	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860	1.000	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917	1.000	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC118912568	0.825	449.6 Da LogP 3.59 TPSA 106.9	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@H]2[C@@H]3CC…`
ZINC118912569	0.825	449.6 Da LogP 3.59 TPSA 106.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@H]2[C@@H]3CC[…`
ZINC1857533486	0.825	449.6 Da LogP 3.59 TPSA 106.9	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@H]2[C@@H]3C…`
ZINC1857533487	0.825	449.6 Da LogP 3.59 TPSA 106.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@H]2[C@@H]3CC…`
ZINC253534396	0.825	449.6 Da LogP 3.59 TPSA 106.9	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@@H]2[C@H]3C…`
ZINC253534397	0.825	449.6 Da LogP 3.59 TPSA 106.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@@H]2[C@H]3CC…`
ZINC257358866	0.825	449.6 Da LogP 3.59 TPSA 106.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@H]2[C@@H]3CC…`
ZINC257358867	0.825	449.6 Da LogP 3.59 TPSA 106.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@H]2[C@@H]3CC…`
ZINC257358868	0.825	449.6 Da LogP 3.59 TPSA 106.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@H]2[C@@H]3CC…`
ZINC257358869	0.825	449.6 Da LogP 3.59 TPSA 106.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@H]2[C@@H]3CC…`
ZINC37245807	0.825	449.6 Da LogP 3.59 TPSA 106.9	✓ Ro5	✓ Clean	`C[C@@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@@H]2[C@H]3C…`
ZINC37245810	0.825	449.6 Da LogP 3.59 TPSA 106.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@@H]1CC[C@@H]2[C@H]3CC…`
ZINC59560281	0.825	449.6 Da LogP 3.59 TPSA 106.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@H]2[C@@H]3CC[…`
ZINC8837267	0.825	449.6 Da LogP 3.59 TPSA 106.9	✓ Ro5	✓ Clean	`C[C@H](CCC(=O)NCC(=O)O)[C@H]1CC[C@H]2[C@@H]3CC[…`
ZINC257357698	0.811	378.6 Da LogP 4.09 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@H](CC(=O)O)[C@@H]1CC[C@@H]2[C@@H]3CC[C@@H]4…`
ZINC31540161	0.811	378.6 Da LogP 4.09 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@H](CC(=O)O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[…`
ZINC118912986	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@H](C)[C@H]1CC[C@H]2[C@@H]3CC[C@H]4C…`
ZINC118912987	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC[C@H]4…`
ZINC119071858	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@H](C)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4…`
ZINC12402838	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@@H](C)[C@@H]1CC[C@@H]2[C@@H]3CC[C@@…`
ZINC12402839	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@H](C)[C@@H]1CC[C@@H]2[C@@H]3CC[C@@H…`
ZINC1857741700	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@H](C)[C@@H]1CC[C@H]2[C@@H]3CC[C@H]4…`
ZINC2160209	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@@H](C)[C@@H]1CC[C@H]2[C@@H]3CC[C@H]…`
ZINC253497499	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@@H](C)[C@@H]1CC[C@@H]2[C@H]3CC[C@H]…`
ZINC253497500	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@H](C)[C@@H]1CC[C@@H]2[C@H]3CC[C@H]4…`
ZINC253497501	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@H](C)[C@@H]1CC[C@@H]2[C@H]3CC[C@H]4…`
ZINC253497502	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@@H](C)[C@@H]1CC[C@@H]2[C@H]3CC[C@H]…`
ZINC253507466	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@H](C)[C@@H]1CC[C@@H]2[C@@H]3CC[C@@H…`
ZINC253507471	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@H](C)[C@@H]1CC[C@@H]2[C@@H]3CC[C@@H…`
ZINC253507477	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@H](C)[C@@H]1CC[C@@H]2[C@@H]3CC[C@@H…`
ZINC253610609	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@@H](C)[C@@H]1CC[C@@H]2[C@@H]3CC[C@@…`
ZINC257359258	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@H](C)[C@@H]1CC[C@@H]2[C@@H]3CC[C@H]…`
ZINC257359259	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@H](C)[C@@H]1CC[C@@H]2[C@@H]3CC[C@H]…`
ZINC257359260	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@H](C)[C@@H]1CC[C@@H]2[C@@H]3CC[C@H]…`
ZINC257359261	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@H](C)[C@@H]1CC[C@@H]2[C@@H]3CC[C@H]…`
ZINC4081644	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@@H](C)[C@H]1CC[C@@H]2[C@@H]3CC[C@H]…`
ZINC4081647	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@@H](C)[C@H]1CC[C@@H]2[C@@H]3CC[C@H]…`
ZINC4429667	0.804	406.6 Da LogP 4.57 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)CC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]…`

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.