Protein profile

PA5411

protein GbcB

Genome: NC_002516.2

Gene: PA5411 gbcB Structure source: AlphaFold UniProt Q9HTF3

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Amino acids 366

Annotations 7

Features 42

PDB binders 6

Druggability 0.669

Overview

Basic information about this protein and its source genome.

Accession: PA5411
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA5411 gbcB
Status: annotated
Amino acids: 366
Structure source: AlphaFold

1.14.13.251

GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0046872 Binding to a metal ion. GO:0004497 Catalysis of the incorporation of one atom of molecular oxygen (O2) into the substrate and the reduction of the other atom of O2 to water. 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:0031457 The chemical reactions and pathways resulting in the breakdown of glycine betaine, N-trimethylglycine. GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 29.299
Human E-value: 5.25e-07
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 0.669

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MSSNFLNPVTTQTWANGRHLVRCVKVIQETWDVRTFCFMADQPILFFFKPGQFVTLELEIDGEPVMRSYTISSSPSVPYSFSITIKRVPGGRVSNWLHDNLKEGQELPVHGPVGLFNAIDFPADKVLFLSGGVGITPVMSMARWFFDTNANVDMVFVHSARSPKDIIYHRELEHMASRIDNFSLHIICERHGLGEAWAGYRGYLNLRMLELIAPDFLEREIFCCGPTPYMSAVKHLLQGHGYDMSRYHEEAFGPTPPEVRADVRELAAEAAEAPEVPVADQHQVEFTATGKSIRVSPGETVHAAAAKLGLHIPKACGMGICGTCKVMKTAGEVEMEHNGGITDEDVAEGYILSCCSVPKGDVVIDY

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1.14.13.251

Gene Ontology (GO)

GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
GO:0046872 Binding to a metal ion.
GO:0004497 Catalysis of the incorporation of one atom of molecular oxygen (O2) into the substrate and the reduction of the other atom of O2 to water.
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:0031457 The chemical reactions and pathways resulting in the breakdown of glycine betaine, N-trimethylglycine.
GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.

Sequence Features

Domain/signature hits from InterPro and related databases.

42 records

Show feature table

Start	End	DB	Term	Name
282	366	ProSiteProfiles	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
282	366	InterPro	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain
290	359	Pfam	PF00111	2Fe-2S iron-sulfur cluster binding domain
290	359	InterPro	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain
21	252	CDD	cd06215	FNR_iron_sulfur_binding_1
220	228	PRINTS	PR00406	Cytochrome B5 reductase signature
127	146	PRINTS	PR00406	Cytochrome B5 reductase signature
164	175	PRINTS	PR00406	Cytochrome B5 reductase signature
104	118	PRINTS	PR00406	Cytochrome B5 reductase signature
67	74	PRINTS	PR00406	Cytochrome B5 reductase signature
120	259	FunFam	G3DSA:3.40.50.80:FF:000056	Probable ferredoxin
120	259	Gene3D	G3DSA:3.40.50.80	-
120	259	InterPro	IPR039261	Ferredoxin-NADP reductase (FNR), nucleotide-binding domain
13	117	SUPERFAMILY	SSF63380	Riboflavin synthase domain-like
13	117	InterPro	IPR017938	Riboflavin synthase-like beta-barrel
13	114	Gene3D	G3DSA:2.40.30.10	Translation factors
16	119	ProSiteProfiles	PS51384	Ferredoxin reductase-type FAD binding domain profile.
16	119	InterPro	IPR017927	FAD-binding domain, ferredoxin reductase-type
128	234	Pfam	PF00175	Oxidoreductase NAD-binding domain
128	234	InterPro	IPR001433	Oxidoreductase FAD/NAD(P)-binding
164	175	PRINTS	PR00371	Flavoprotein pyridine nucleotide cytochrome reductase signature
164	175	InterPro	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase
127	146	PRINTS	PR00371	Flavoprotein pyridine nucleotide cytochrome reductase signature
127	146	InterPro	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase
220	228	PRINTS	PR00371	Flavoprotein pyridine nucleotide cytochrome reductase signature
220	228	InterPro	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase
67	74	PRINTS	PR00371	Flavoprotein pyridine nucleotide cytochrome reductase signature
67	74	InterPro	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase
25	116	Pfam	PF00970	Oxidoreductase FAD-binding domain
25	116	InterPro	IPR008333	Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain
316	324	ProSitePatterns	PS00197	2Fe-2S ferredoxin-type iron-sulfur binding region signature.
316	324	InterPro	IPR006058	2Fe-2S ferredoxin, iron-sulphur binding site
243	365	SUPERFAMILY	SSF54292	2Fe-2S ferredoxin-like
243	365	InterPro	IPR036010	2Fe-2S ferredoxin-like superfamily
289	365	CDD	cd00207	fer2
289	365	InterPro	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain
17	365	PANTHER	PTHR47354	NADH OXIDOREDUCTASE HCR
263	366	FunFam	G3DSA:3.10.20.30:FF:000041	Glycine-betaine demethylase subunit GbcB
108	250	SUPERFAMILY	SSF52343	Ferredoxin reductase-like, C-terminal NADP-linked domain
108	250	InterPro	IPR039261	Ferredoxin-NADP reductase (FNR), nucleotide-binding domain
263	366	Gene3D	G3DSA:3.10.20.30	-
263	366	InterPro	IPR012675	Beta-grasp 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 PA5411	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				0.669

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.

56 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
DGG	1CQX	P39662	735.0 Da LogP 9.75 TPSA 148.8	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@…`
ECN	3OZV	P39662	381.7 Da LogP 5.80 TPSA 27.1	1 viol.	✓ Clean	`c1cc(ccc1COC(Cn2ccnc2)c3ccc(cc3Cl)Cl)Cl`
FDA	1TVC	P22868	787.6 Da LogP -1.75 TPSA 363.3	3 viol.	✓ Clean	`Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C…`
FES	6LAA	A0A0K6ITW2	175.8 Da LogP 1.29 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]S[Fe]1`
KKK	3OZW	P39662	531.4 Da LogP 4.21 TPSA 69.1	1 viol.	Alert	`CC(=O)N1CCN(CC1)c2ccc(cc2)OC[C@H]3CO[C@](O3)(Cn…`
X89	3OZU	P39662	416.1 Da LogP 6.45 TPSA 27.1	1 viol.	✓ Clean	`c1cc(c(cc1Cl)Cl)CO[C@@H](Cn2ccnc2)c3ccc(cc3Cl)Cl`

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
ZINC102191119	0.824	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@@H](O)CO…`
ZINC58649551	0.824	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@H](O)CO)…`
ZINC28568236	0.795	489.4 Da LogP 3.95 TPSA 60.8	✓ Ro5	Alert	`Clc1ccc([C@@]2(Cn3ccnc3)OC[C@H](COc3ccc(N4CCNCC…`
ZINC31416683	0.795	489.4 Da LogP 3.95 TPSA 60.8	✓ Ro5	Alert	`Clc1ccc([C@]2(Cn3ccnc3)OC[C@@H](COc3ccc(N4CCNCC…`
ZINC38944078	0.795	489.4 Da LogP 3.95 TPSA 60.8	✓ Ro5	Alert	`Clc1ccc([C@]2(Cn3ccnc3)OC[C@H](COc3ccc(N4CCNCC4…`
ZINC38944080	0.795	489.4 Da LogP 3.95 TPSA 60.8	✓ Ro5	Alert	`Clc1ccc([C@@]2(Cn3ccnc3)OC[C@@H](COc3ccc(N4CCNC…`
ZINC1532199	0.729	297.2 Da LogP 4.13 TPSA 27.1	✓ Ro5	✓ Clean	`C=CCO[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC1532200	0.729	297.2 Da LogP 4.13 TPSA 27.1	✓ Ro5	✓ Clean	`C=CCO[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC95918118	0.673	312.8 Da LogP 4.49 TPSA 27.1	✓ Ro5	✓ Clean	`Clc1ccc(CO[C@H](Cn2ccnc2)c2ccccc2)cc1`
ZINC95918119	0.673	312.8 Da LogP 4.49 TPSA 27.1	✓ Ro5	✓ Clean	`Clc1ccc(CO[C@@H](Cn2ccnc2)c2ccccc2)cc1`
ZINC102191158	0.660	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OC[C@…`
ZINC14880758	0.660	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OC[…`
ZINC14880760	0.660	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OC[C…`
ZINC53683910	0.660	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OC[…`
ZINC62592202	0.660	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OC[C@…`
ZINC62592203	0.660	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC[C…`
ZINC62592204	0.660	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC…`
ZINC96094841	0.660	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC[C…`
ZINC849188212	0.654	327.2 Da LogP 4.13 TPSA 44.1	✓ Ro5	✓ Clean	`CC(C)C(=O)O[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC849188213	0.654	327.2 Da LogP 4.13 TPSA 44.1	✓ Ro5	✓ Clean	`CC(C)C(=O)O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC38334168	0.649	407.3 Da LogP 2.43 TPSA 79.7	✓ Ro5	✓ Clean	`CS(=O)(=O)OC[C@@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc…`
ZINC198375289	0.635	299.2 Da LogP 3.49 TPSA 44.1	✓ Ro5	✓ Clean	`CC(=O)O[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC198375301	0.635	299.2 Da LogP 3.49 TPSA 44.1	✓ Ro5	✓ Clean	`CC(=O)O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC5349880	0.628	433.3 Da LogP 4.32 TPSA 62.6	✓ Ro5	✓ Clean	`O=C(OC[C@@H]1CO[C@@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O…`
ZINC5349883	0.628	433.3 Da LogP 4.32 TPSA 62.6	✓ Ro5	✓ Clean	`O=C(OC[C@H]1CO[C@@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1…`
ZINC638711	0.628	433.3 Da LogP 4.32 TPSA 62.6	✓ Ro5	✓ Clean	`O=C(OC[C@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1)…`
ZINC638717	0.628	433.3 Da LogP 4.32 TPSA 62.6	✓ Ro5	✓ Clean	`O=C(OC[C@@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1…`
ZINC297645	0.620	329.2 Da LogP 2.45 TPSA 56.5	✓ Ro5	✓ Clean	`OC[C@@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1`
ZINC297649	0.620	329.2 Da LogP 2.45 TPSA 56.5	✓ Ro5	✓ Clean	`OC[C@@H]1CO[C@@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1`
ZINC297652	0.620	329.2 Da LogP 2.45 TPSA 56.5	✓ Ro5	✓ Clean	`OC[C@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1`
ZINC297656	0.620	329.2 Da LogP 2.45 TPSA 56.5	✓ Ro5	✓ Clean	`OC[C@H]1CO[C@@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1`
ZINC102190506	0.614	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCCN)OC(=O)CC…`
ZINC102190512	0.614	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)C…`
ZINC4217243	0.605	367.2 Da LogP 3.11 TPSA 45.5	✓ Ro5	✓ Clean	`C#CCOC[C@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1`
ZINC390893	0.604	257.1 Da LogP 2.92 TPSA 38.0	✓ Ro5	✓ Clean	`O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC390894	0.604	257.1 Da LogP 2.92 TPSA 38.0	✓ Ro5	✓ Clean	`O[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC21988957	0.600	483.4 Da LogP 4.17 TPSA 79.7	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@H]2CO[C@](Cn3ccnc3)(c3ccc(…`
ZINC22057057	0.600	483.4 Da LogP 4.17 TPSA 79.7	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@@H]2CO[C@@](Cn3ccnc3)(c3cc…`
ZINC22057060	0.600	483.4 Da LogP 4.17 TPSA 79.7	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@@H]2CO[C@](Cn3ccnc3)(c3ccc…`
ZINC6088320	0.600	483.4 Da LogP 4.17 TPSA 79.7	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@H]2CO[C@@](Cn3ccnc3)(c3ccc…`
ZINC849187659	0.600	325.2 Da LogP 3.88 TPSA 44.1	✓ Ro5	✓ Clean	`O=C(O[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl)C1CC1`
ZINC849187660	0.600	325.2 Da LogP 3.88 TPSA 44.1	✓ Ro5	✓ Clean	`O=C(O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl)C1CC1`
ZINC27416437	0.596	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCCN)OC(=O)CCCCC`
ZINC33902364	0.596	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)CCC…`
ZINC36178999	0.593	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC36179002	0.593	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC849188227	0.589	341.2 Da LogP 4.52 TPSA 44.1	✓ Ro5	✓ Clean	`CC(C)CC(=O)O[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC849188228	0.589	341.2 Da LogP 4.52 TPSA 44.1	✓ Ro5	✓ Clean	`CC(C)CC(=O)O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC849188298	0.589	355.3 Da LogP 4.91 TPSA 44.1	✓ Ro5	✓ Clean	`CCC(CC)C(=O)O[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC849188301	0.589	355.3 Da LogP 4.91 TPSA 44.1	✓ Ro5	✓ Clean	`CCC(CC)C(=O)O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`

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.