Protein profile

PA5355

glycolate oxidase subunit GlcD

Genome: NC_002516.2

Gene: glcD PA5355 Structure source: AlphaFold UniProt Q9HTK3

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Amino acids 499

Annotations 7

Features 21

PDB binders 15

Druggability 0.828

Overview

Basic information about this protein and its source genome.

Accession: PA5355
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: glcD PA5355
Status: annotated
Amino acids: 499
Structure source: AlphaFold

GO:0009339 An enzyme complex that catalyzes the oxidation of 2-hydroxy acid to form 2-oxo acid and H2O2. The enzyme is a flavoprotein (FMN). GO:0003973 Catalysis of the reaction: (S)-2-hydroxy-acid + O2 = 2-oxo acid + H2O2. GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes. GO:0019154 Catalysis of the reaction: A + glycolate = AH(2) + glyoxylate. GO:0046296 The chemical reactions and pathways resulting in the breakdown of glycolate, the anion of hydroxyethanoic acid (glycolic acid). GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 39.583
Human E-value: 3.13e-12
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 0.828

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

GO:0009339 An enzyme complex that catalyzes the oxidation of 2-hydroxy acid to form 2-oxo acid and H2O2. The enzyme is a flavoprotein (FMN).
GO:0003973 Catalysis of the reaction: (S)-2-hydroxy-acid + O2 = 2-oxo acid + H2O2.
GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
GO:0019154 Catalysis of the reaction: A + glycolate = AH(2) + glyoxylate.
GO:0046296 The chemical reactions and pathways resulting in the breakdown of glycolate, the anion of hydroxyethanoic acid (glycolic acid).
GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
231	344	Gene3D	G3DSA:3.30.70.2190	-
11	108	Gene3D	G3DSA:3.30.43.10	-
11	108	InterPro	IPR016167	FAD-binding, type PCMH, subdomain 1
231	470	Pfam	PF02913	FAD linked oxidases, C-terminal domain
231	470	InterPro	IPR004113	FAD-binding oxidoreductase/transferase, type 4, C-terminal
204	473	SUPERFAMILY	SSF55103	FAD-linked oxidases, C-terminal domain
204	473	InterPro	IPR016164	FAD-linked oxidase-like, C-terminal
56	194	Pfam	PF01565	FAD binding domain
56	194	InterPro	IPR006094	FAD linked oxidase, N-terminal
432	471	Gene3D	G3DSA:1.10.45.10	-
432	471	InterPro	IPR016171	Vanillyl-alcohol oxidase, C-terminal subdomain 2
350	431	Gene3D	G3DSA:3.30.70.2740	-
52	230	ProSiteProfiles	PS51387	PCMH-type FAD-binding domain profile.
52	230	InterPro	IPR016166	FAD-binding domain, PCMH-type
110	230	Gene3D	G3DSA:3.30.465.10	-
110	230	InterPro	IPR016169	FAD-binding, type PCMH, subdomain 2
14	488	PANTHER	PTHR42934	GLYCOLATE OXIDASE SUBUNIT GLCD
19	231	SUPERFAMILY	SSF56176	FAD-binding/transporter-associated domain-like
19	231	InterPro	IPR036318	FAD-binding, type PCMH-like superfamily
59	470	NCBIfam	TIGR00387	glycolate oxidase subunit GlcD
59	470	InterPro	IPR004490	Glycolate oxidase subunit GlcD

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 PA5355	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				0.828
3				0.42

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.

66 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
1DO	4BC7	P97275	186.3 Da LogP 3.90 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCO`
2HG	6LPP	Q8N465	148.1 Da LogP -0.70 TPSA 94.8	✓ Ro5	✓ Clean	`C(CC(=O)O)[C@H](C(=O)O)O`
AKG	6LPX	Q8N465	146.1 Da LogP -0.50 TPSA 91.7	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)C(=O)O`
AWB	5AE3	P97275	548.6 Da LogP 3.48 TPSA 157.3	1 viol.	✓ Clean	`CCCCCC[C@@H]1[C@H]([C@@H](OC(=O)[C@H]([C@H](OC1…`
B2Z	5AE1	P97275	341.4 Da LogP 3.37 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@@H](CC(=O)N[C@H](C)c1ccc2c(c1)NC(=O)N2)c3cc…`
BEZ	5FXF	Q0SBK1	122.1 Da LogP 1.38 TPSA 37.3	✓ Ro5	✓ Clean	`c1ccc(cc1)C(=O)O`
CIY	5FXE	Q0SBK1	178.2 Da LogP 1.61 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(ccc1O)/C=C/C=O`
F6T	6GOU	P97275	345.3 Da LogP 2.94 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@@H](CC(=O)NCc1ccc2c(c1)NC(=O)N2)c3c(cccc3F)F`
FYC	5AE2	P97275	325.3 Da LogP 2.71 TPSA 77.8	✓ Ro5	✓ Clean	`C/C(=C\c1ccccc1F)/C(=O)NCc2ccc3c(c2)NC(=O)N3`
KQS	5ADZ	P97275	327.4 Da LogP 2.81 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@@H](CC(=O)NCc1ccc2c(c1)NC(=O)N2)c3ccccc3F`
LAC	6LPT	Q8N465	90.1 Da LogP -0.55 TPSA 57.5	✓ Ro5	✓ Clean	`C[C@H](C(=O)O)O`
MLT	6LPQ	Q8N465	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)O)C(=O)O`
PL3	2UUU	O96759	242.4 Da LogP 5.46 TPSA 20.2	1 viol.	✓ Clean	`CCCCCCCCCCCCCCCCO`
S2G	6LPU	Q8N465	148.1 Da LogP -0.70 TPSA 94.8	✓ Ro5	✓ Clean	`C(CC(=O)O)[C@@H](C(=O)O)O`
V55	5FXP	Q0SBK1	152.1 Da LogP 1.21 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(ccc1O)C=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
CHEMBL4563407	O00116	—	345.3 Da LogP 2.94 TPSA 77.8	✓ Ro5	✓ Clean	`CC(CC(=O)NCc1ccc2[nH]c(=O)[nH]c2c1)c1c(F)cccc1F`

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
ZINC1644076	1.000	214.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCO`
ZINC1680803	1.000	200.4 Da LogP 4.29 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCO`
ZINC69435448	1.000	341.4 Da LogP 3.37 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@@H](CC(=O)N[C@@H](C)c1ccc2[nH]c(=O)[nH]c2c1…`
ZINC69435452	1.000	341.4 Da LogP 3.37 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@H](NC(=O)C[C@@H](C)c1ccccc1F)c1ccc2[nH]c(=O…`
ZINC69435458	1.000	341.4 Da LogP 3.37 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@@H](CC(=O)N[C@H](C)c1ccc2[nH]c(=O)[nH]c2c1)…`
ZINC69435460	1.000	341.4 Da LogP 3.37 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@H](CC(=O)N[C@H](C)c1ccc2[nH]c(=O)[nH]c2c1)c…`
ZINC3269660	0.824	254.2 Da LogP 2.45 TPSA 71.4	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC2504355	0.778	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccccc2)cc1`
ZINC185070	0.733	272.3 Da LogP 3.29 TPSA 58.9	✓ Ro5	✓ Clean	`COc1cc(/C=C/c2ccc(O)c(OC)c2)ccc1O`
ZINC1672966	0.688	210.2 Da LogP 2.75 TPSA 34.1	✓ Ro5	Alert	`O=C(C(=O)c1ccccc1)c1ccccc1`
ZINC2149802	0.684	210.4 Da LogP 3.90 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCC#CCCCCCCO`
ZINC2555300	0.684	238.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCC#CCCCCCCCCO`
ZINC2579260	0.684	238.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCCC#CCCCCCCO`
ZINC34057267	0.684	274.3 Da LogP 4.72 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccccc3)cc2)cc1`
ZINC59724910	0.684	212.4 Da LogP 4.46 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCC/C=C/CCCCO`
ZINC59724924	0.684	212.4 Da LogP 4.46 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCO`
ZINC59724927	0.684	212.4 Da LogP 4.46 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCO`
ZINC95831576	0.684	230.4 Da LogP 3.92 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCCCO`
ZINC1857579176	0.679	345.3 Da LogP 3.36 TPSA 78.0	✓ Ro5	✓ Clean	`C[C@H](CC(=O)NCc1ccc2nc(O)[nH]c2c1)c1c(F)cccc1F`
ZINC1857606065	0.679	345.3 Da LogP 3.36 TPSA 78.0	✓ Ro5	✓ Clean	`C[C@@H](CC(=O)NCc1ccc2nc(O)[nH]c2c1)c1c(F)cccc1F`
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`
ZINC114185151	0.647	298.2 Da LogP 2.15 TPSA 108.7	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC13541228	0.647	258.3 Da LogP 2.98 TPSA 69.9	✓ Ro5	✓ Clean	`COc1cc(/C=C/c2cc(O)cc(O)c2)ccc1O`
ZINC1590838	0.647	342.4 Da LogP 3.82 TPSA 68.3	✓ Ro5	Alert	`O=C(C(=O)c1ccc(C(=O)C(=O)c2ccccc2)cc1)c1ccccc1`
ZINC16133932	0.647	474.5 Da LogP 4.88 TPSA 102.4	✓ Ro5	Alert	`O=C(C(=O)c1ccc(C(=O)C(=O)c2ccc(C(=O)C(=O)c3cccc…`
ZINC2053487767	0.647	258.3 Da LogP 2.98 TPSA 69.9	✓ Ro5	✓ Clean	`COc1cc(C=Cc2cc(O)cc(O)c2)ccc1O`
ZINC1635826	0.645	300.3 Da LogP 2.57 TPSA 83.6	✓ Ro5	Alert	`COc1cc(/C=N/N=C/c2ccc(O)c(OC)c2)ccc1O`
ZINC16997495	0.645	300.3 Da LogP 2.57 TPSA 83.6	✓ Ro5	Alert	`COc1cc(/C=N\N=C/c2ccc(O)c(OC)c2)ccc1O`
ZINC254438868	0.645	300.3 Da LogP 2.57 TPSA 83.6	✓ Ro5	Alert	`COc1cc(C=NN=Cc2ccc(O)c(OC)c2)ccc1O`
ZINC5022931	0.645	300.3 Da LogP 2.57 TPSA 83.6	✓ Ro5	Alert	`COc1cc(/C=N\N=C\c2ccc(O)c(OC)c2)ccc1O`
ZINC49033638	0.635	287.2 Da LogP 1.99 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@H](NC(=O)CC(F)(F)F)c1ccc2[nH]c(=O)[nH]c2c1`
ZINC49033640	0.635	287.2 Da LogP 1.99 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)CC(F)(F)F)c1ccc2[nH]c(=O)[nH]c2c1`
ZINC120595	0.629	226.3 Da LogP 3.57 TPSA 29.5	✓ Ro5	✓ Clean	`COc1cc(/C=C/c2ccccc2)ccc1O`
ZINC5081027	0.629	226.3 Da LogP 3.57 TPSA 29.5	✓ Ro5	✓ Clean	`COc1cc(/C=C\c2ccccc2)ccc1O`
ZINC54009977	0.623	313.3 Da LogP 2.42 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@H](NC(=O)Cc1ccc(F)cc1)c1ccc2[nH]c(=O)[nH]c2…`
ZINC54009978	0.623	313.3 Da LogP 2.42 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)Cc1ccc(F)cc1)c1ccc2[nH]c(=O)[nH]c…`
ZINC12358996	0.622	208.2 Da LogP 1.59 TPSA 55.8	✓ Ro5	✓ Clean	`COC(=O)/C=C\c1ccc(O)c(OC)c1`
ZINC1621053	0.622	208.2 Da LogP 1.59 TPSA 55.8	✓ Ro5	✓ Clean	`COC(=O)/C=C/c1ccc(O)c(OC)c1`
ZINC17255287	0.622	368.4 Da LogP 3.37 TPSA 93.1	✓ Ro5	✓ Clean	`COc1cc(/C=C\C(=O)CC(=O)/C=C/c2ccc(O)c(OC)c2)ccc…`
ZINC1857743026	0.622	368.4 Da LogP 3.37 TPSA 93.1	✓ Ro5	✓ Clean	`COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O`
ZINC1903846672	0.622	208.2 Da LogP 1.59 TPSA 55.8	✓ Ro5	✓ Clean	`COC(=O)C=Cc1ccc(O)c(OC)c1`
ZINC31261437	0.622	368.4 Da LogP 3.37 TPSA 93.1	✓ Ro5	✓ Clean	`COc1cc(/C=C\C(=O)CC(=O)/C=C\c2ccc(O)c(OC)c2)ccc…`
ZINC899824	0.622	368.4 Da LogP 3.37 TPSA 93.1	✓ Ro5	✓ Clean	`COc1cc(/C=C/C(=O)CC(=O)/C=C/c2ccc(O)c(OC)c2)ccc…`
ZINC100244447	0.619	276.5 Da LogP 4.04 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[S@@](=O)CCCCCCCO`
ZINC100244449	0.619	276.5 Da LogP 4.04 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[S@](=O)CCCCCCCO`
ZINC98008412	0.619	250.4 Da LogP 2.53 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)CCCCO`
ZINC98008413	0.619	234.4 Da LogP 2.87 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[S@@](=O)CCCCO`
ZINC98008414	0.619	234.4 Da LogP 2.87 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[S@](=O)CCCCO`

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.