Protein profile

PA5418

sarcosine oxidase subunit alpha

Genome: NC_002516.2

Gene: soxA PA5418 Structure source: AlphaFold UniProt Q9HTE6

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Amino acids 1005

Annotations 7

Features 34

PDB binders 7

Druggability 0.65

Overview

Basic information about this protein and its source genome.

Accession: PA5418
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: soxA PA5418
Status: annotated
Amino acids: 1005
Structure source: AlphaFold

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0047545 Catalysis of the reaction: (S)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor. GO:0008115 Catalysis of the reaction: H2O + O2 + sarcosine = formaldehyde + glycine + H2O2. GO:1901053 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of sarcosine. GO:0046653 The chemical reactions and pathways involving tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group. 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 (%): 33.708
Human E-value: 9.26e-06
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 0.65

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MSQINRLSSGGRIDRNRPLTFSFNGQHYQGYAGDTLAAALLANGVDIVGRSFKYSRARGIVAAGAEEPNAILQIGSREATQIPNVRATQQALYGGLVATSTNGWPNVQNDLMGIFGKVGGKLMPPGFYYKTFMYPQSMWMTYEKYIRKAAGLGRAPTEVDPDSYDWMNHHCDVLVVGAGPAGLAAALAAARSGARVILADEQEEFGGSLLDTRETLDGKPAAEWVADAVAELQGLPEVILLPRSTVNGYHDHNFLTIHERRTDHLGEVAPLGQVRQRVHRVRAKRVVLAAGAHERPLVYGNNDLPGNMLAGAVSTYVRRYGVAPGKKLVLATNNDYAYRVALDWQEAGLQVVAIADARANPRGEWVEEARQRGMRVITGSSVIEARGGKRVSGAKVARIDLQAMRASGGEWLDCDLIASSGGYSPVVHLASHLGGKPEWREEILAFVPGEGLQKRICAGAVNGVFGLAEVLADGYQAGSRAALDAGYKTAAGSLPKVQPRREEASVALFQVPHEKPTARAPKQFVDPQNDVTAAAIELACREGFESIEHVKRYTALGFGTDQGKLGNINGLAIAARAQGKSIADTGTTMFRPNYTPVTFGAVAGRHCGHLFEPVRFTALHAWHVKNGAEFEDVGQWKRPWYFPRRGEDMHAAVARECRAVREAVGLLDASTLGKIDIQGPDAREFLNRVYTNAWTKLDVGKARYGLMCKEDGMVFDDGVTACLADNHFVMTTTTGGAARVLEWLELYHQTEWPELKVYFTSVTDHYATLTLSGPNSRKLLAEVTDIDLDKDAFPFMTWKEGKVAGVPARVFRISFTGELSYEVNVQADYAMGVLEALAEHGAKYGLTPYGTETMHVLRAEKGFIIVGQDTDASVTPDDLNMGWAVGRSKPFSWIGWRGMNRADCLREDRKQLVGLRPSNPQEVLPEGAQLVFDTQQAIPMKMVGHVTSSYMSASLGHGFALAVVKGGLKRMGQKVYAPLADGRFIEAEICSSVFYDPKGERQNVD

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0047545 Catalysis of the reaction: (S)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor.
GO:0008115 Catalysis of the reaction: H2O + O2 + sarcosine = formaldehyde + glycine + H2O2.
GO:1901053 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of sarcosine.
GO:0046653 The chemical reactions and pathways involving tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
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.
GO:0005515 Binding to a protein.

Sequence Features

Domain/signature hits from InterPro and related databases.

34 records

Show feature table

Start	End	DB	Term	Name
619	884	Pfam	PF01571	Aminomethyltransferase folate-binding domain
619	884	InterPro	IPR006222	Aminomethyltransferase, folate-binding domain
1	948	PANTHER	PTHR43104	L-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL
613	895	SUPERFAMILY	SSF103025	Folate-binding domain
10	104	Gene3D	G3DSA:3.10.20.440	-
10	104	InterPro	IPR042204	2Fe-2S iron-sulfur cluster binding domain, N-terminal
521	604	Pfam	PF17806	Sarcosine oxidase A3 domain
521	604	InterPro	IPR041117	SoxA, A3 domain
2	1004	NCBIfam	TIGR01372	sarcosine oxidase subunit alpha family protein
2	1004	InterPro	IPR006277	Sarcosine oxidase, alpha subunit
283	301	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
173	192	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
167	448	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
167	448	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
167	317	Gene3D	G3DSA:3.50.50.60	-
167	317	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
614	1004	Gene3D	G3DSA:3.30.1360.120	Probable tRNA modification gtpase trme; domain 1
614	1004	InterPro	IPR027266	GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1
614	1004	FunFam	G3DSA:3.30.1360.120:FF:000038	Sarcosine oxidase subunit alpha
167	317	FunFam	G3DSA:3.50.50.60:FF:000476	Sarcosine oxidase subunit alpha
906	1003	SUPERFAMILY	SSF101790	Aminomethyltransferase beta-barrel domain
906	1003	InterPro	IPR029043	Glycine cleavage T-protein/YgfZ, C-terminal
527	585	Gene3D	G3DSA:1.10.10.1100	-
527	585	InterPro	IPR041854	BFD-like [2Fe-2S]-binding domain superfamily
284	292	PRINTS	PR00469	Pyridine nucleotide disulphide reductase class-II signature
459	477	PRINTS	PR00469	Pyridine nucleotide disulphide reductase class-II signature
172	194	PRINTS	PR00469	Pyridine nucleotide disulphide reductase class-II signature
910	996	Pfam	PF08669	Glycine cleavage T-protein C-terminal barrel domain
910	996	InterPro	IPR013977	Glycine cleavage T-protein, C-terminal barrel domain
1	1004	PIRSF	PIRSF037980	Sarcos_oxid_alpha
1	1004	InterPro	IPR006277	Sarcosine oxidase, alpha subunit
17	102	Pfam	PF13510	2Fe-2S iron-sulfur cluster binding domain
172	434	Pfam	PF07992	Pyridine nucleotide-disulphide oxidoreductase
172	434	InterPro	IPR023753	FAD/NAD(P)-binding domain

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

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA5418	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				0.65
1				0.229

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.

57 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
DMG	1VRQ	Q50LF0	103.1 Da LogP -0.37 TPSA 40.5	✓ Ro5	✓ Clean	`CN(C)CC(=O)O`
FFO	1PJ7	Q9AGP8	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)NCC2CNC3=C(N2C…`
FOA	2GAG	Q3ZDQ8	112.1 Da LogP 0.98 TPSA 50.4	✓ Ro5	✓ Clean	`c1cc(oc1)C(=O)O`
FOL	1PJ6	Q9AGP8	441.4 Da LogP -0.04 TPSA 213.3	1 viol.	✓ Clean	`c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NCc2cnc3c…`
FON	1VRQ	Q50LF0	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@@H]2…`
RED	1WOR	Q9WY54	208.3 Da LogP 2.25 TPSA 37.3	✓ Ro5	✓ Clean	`C(CCC(=O)O)C[C@H](CCS)S`
THG	4PAA	Q63342	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@H]2C…`

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).

No ChEMBL hits found through similar proteins.

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
ZINC1529363	1.000	208.3 Da LogP 2.25 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCC[C@H](S)CCS`
ZINC3869601	1.000	208.3 Da LogP 2.25 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCC[C@@H](S)CCS`
ZINC9212425	0.803	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…`
ZINC9212426	0.803	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…`
ZINC9212427	0.803	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…`
ZINC9212428	0.803	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…`
ZINC200768381	0.727	344.3 Da LogP -0.08 TPSA 153.4	✓ Ro5	✓ Clean	`Nc1nc(=O)c2c([nH]1)NC[C@@H](CNc1ccc(C(=O)O)cc1)…`
ZINC200768411	0.727	344.3 Da LogP -0.08 TPSA 153.4	✓ Ro5	✓ Clean	`Nc1nc(=O)c2c([nH]1)NC[C@H](CNc1ccc(C(=O)O)cc1)N…`
ZINC8628600	0.716	473.5 Da LogP 0.13 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c([nH]c(N)nc2=O)NC[C@@H]1CCNc1ccc(C(=O)N[C…`
ZINC8628601	0.716	473.5 Da LogP 0.13 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c([nH]c(N)nc2=O)NC[C@H]1CCNc1ccc(C(=O)N[C@…`
ZINC8655682	0.688	487.5 Da LogP -0.34 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CCNc1ccc(C(=O)N…`
ZINC85394426	0.667	206.2 Da LogP 1.80 TPSA 80.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccco2)o1`
ZINC8997303	0.667	487.5 Da LogP 0.07 TPSA 220.1	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@@H](CNc1ccc(C(=O)N[C@@H](CC…`
ZINC8997304	0.667	487.5 Da LogP 0.07 TPSA 220.1	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@@H](CNc1ccc(C(=O)N[C@H](CCC…`
ZINC8997305	0.667	487.5 Da LogP 0.07 TPSA 220.1	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@H](CNc1ccc(C(=O)N[C@@H](CCC…`
ZINC8997306	0.667	487.5 Da LogP 0.07 TPSA 220.1	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@H](CNc1ccc(C(=O)N[C@H](CCCC…`
ZINC2005305	0.658	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…`
ZINC2572666	0.658	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@@…`
ZINC4228266	0.658	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…`
ZINC4228267	0.658	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@H…`
ZINC12374887	0.630	216.2 Da LogP 2.21 TPSA 67.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccco2)cc1`
ZINC169748282	0.623	471.4 Da LogP -0.26 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc(=O)c2c([nH]1)NC=C(CNc1ccc(C(=O)N[C@@H](CC…`
ZINC1710770	0.615	200.2 Da LogP 2.35 TPSA 47.3	✓ Ro5	Alert	`O=C(C(=O)c1ccco1)c1ccccc1`
ZINC8655681	0.613	487.5 Da LogP 0.07 TPSA 220.1	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@@H](CCNc1ccc(C(=O)N[C@@H](C…`
ZINC8655685	0.613	487.5 Da LogP 0.07 TPSA 220.1	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@H](CCNc1ccc(C(=O)N[C@H](CCC…`
ZINC8667682	0.613	487.5 Da LogP 0.07 TPSA 220.1	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@@H](CCNc1ccc(C(=O)N[C@H](CC…`
ZINC223670610	0.610	459.5 Da LogP -0.28 TPSA 194.0	1 viol.	✓ Clean	`CN(c1ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)cc1)[C@@H…`
ZINC3870062	0.610	457.4 Da LogP -0.52 TPSA 194.0	1 viol.	✓ Clean	`Nc1nc(=O)c2c([nH]1)NC[C@H]1CN(c3ccc(C(=O)N[C@H]…`
ZINC1613560	0.607	216.2 Da LogP 2.21 TPSA 67.5	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1ccco1`
ZINC100477623	0.600	204.2 Da LogP 2.33 TPSA 60.4	✓ Ro5	✓ Clean	`O=C(CC(=O)c1ccco1)c1ccco1`
ZINC1637602	0.600	443.5 Da LogP 0.62 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc(=O)c2c([nH]1)NC[C@@H](CCc1ccc(C(=O)N[C@@H…`
ZINC6472822	0.600	218.2 Da LogP 2.72 TPSA 60.4	✓ Ro5	✓ Clean	`O=C(CCC(=O)c1ccco1)c1ccco1`
ZINC4228235	0.597	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@@H](…`
ZINC4228236	0.597	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@H](C…`
ZINC4228237	0.597	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@@H]…`
ZINC4228238	0.597	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@H](…`
ZINC156403	0.593	274.3 Da LogP 1.47 TPSA 66.9	✓ Ro5	✓ Clean	`O=C(c1ccco1)N1CCN(C(=O)c2ccco2)CC1`
ZINC8536462	0.587	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc(=O)c2c([nH]1)NC[C@H](CN(C=O)c1ccc(C(=O)N[…`
ZINC19367002	0.579	204.2 Da LogP -0.98 TPSA 81.1	✓ Ro5	✓ Clean	`CN(CCN(C)CC(=O)O)CC(=O)O`
ZINC12496906	0.577	457.4 Da LogP 0.22 TPSA 202.8	1 viol.	✓ Clean	`CN1C(CNc2ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)cc2)=…`
ZINC983943	0.577	360.3 Da LogP 4.16 TPSA 90.6	✓ Ro5	✓ Clean	`O=C(c1cc(C(=O)c2ccco2)cc(C(=O)c2ccco2)c1)c1ccco1`
ZINC106891773	0.571	204.2 Da LogP 2.65 TPSA 63.6	✓ Ro5	✓ Clean	`O=C(/C=C(\O)c1ccco1)c1ccco1`
ZINC19364891	0.571	204.2 Da LogP -0.98 TPSA 81.1	✓ Ro5	✓ Clean	`CN(C)CCN(CC(=O)O)CC(=O)O`
ZINC49815930	0.567	216.2 Da LogP 2.21 TPSA 67.5	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)c2ccco2)c1`
ZINC13511874	0.561	475.5 Da LogP -2.28 TPSA 215.5	1 viol.	✓ Clean	`NC1=NC(=O)[C@@H]2[C@@H](NC[C@@H](CNc3ccc(C(=O)N…`
ZINC13511881	0.561	475.5 Da LogP -2.28 TPSA 215.5	1 viol.	✓ Clean	`NC1=NC(=O)[C@@H]2[C@H](NC[C@@H](CNc3ccc(C(=O)N[…`
ZINC252485840	0.561	475.5 Da LogP -2.28 TPSA 215.5	1 viol.	✓ Clean	`NC1=NC(=O)[C@@H]2[C@H](NC[C@H](CNc3ccc(C(=O)N[C…`
ZINC252485841	0.561	475.5 Da LogP -2.28 TPSA 215.5	1 viol.	✓ Clean	`NC1=NC(=O)[C@@H]2[C@H](NC[C@@H](CNc3ccc(C(=O)N[…`
ZINC55201	0.556	298.2 Da LogP 3.31 TPSA 78.9	✓ Ro5	✓ Clean	`O=C(Oc1ccc(OC(=O)c2ccco2)cc1)c1ccco1`
ZINC95097410	0.552	214.2 Da LogP 2.74 TPSA 47.3	✓ Ro5	✓ Clean	`O=C(CC(=O)c1ccco1)c1ccccc1`

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.