Protein profile

PA4807

selenocysteine-specific elongation factor

Genome: NC_002516.2

Gene: selB PA4807 Structure source: AlphaFold UniProt Q9HV02

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Amino acids 641

Annotations 8

Features 50

PDB binders 6

Druggability 0.559

Overview

Basic information about this protein and its source genome.

Accession: PA4807
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: selB PA4807
Status: annotated
Amino acids: 641
Structure source: AlphaFold

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005525 Binding to GTP, guanosine triphosphate. GO:0003924 Catalysis of the reaction: GTP + H2O = GDP + H+ + phosphate. GO:0035368 Binding to a selenocysteine insertion sequence (SECIS), a regulatory sequence within mRNA which directs incorporation of a selenocysteine at a stop codon (UGA) during translation. GO:0003746 Functions in chain elongation during polypeptide synthesis at the ribosome. GO:0001514 The incorporation of selenocysteine into a peptide; uses a special tRNA that recognizes the UGA codon as selenocysteine, rather than as a termination codon. Selenocysteine is synthesized from serine before its incorporation; it is not a posttranslational modification of peptidyl-cysteine.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 40.698
Human E-value: 1.36e-10
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 0.559

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0005525 Binding to GTP, guanosine triphosphate.
GO:0003924 Catalysis of the reaction: GTP + H2O = GDP + H+ + phosphate.
GO:0035368 Binding to a selenocysteine insertion sequence (SECIS), a regulatory sequence within mRNA which directs incorporation of a selenocysteine at a stop codon (UGA) during translation.
GO:0003746 Functions in chain elongation during polypeptide synthesis at the ribosome.
GO:0001514 The incorporation of selenocysteine into a peptide; uses a special tRNA that recognizes the UGA codon as selenocysteine, rather than as a termination codon. Selenocysteine is synthesized from serine before its incorporation; it is not a posttranslational modification of peptidyl-cysteine.
GO:0016259 OBSOLETE. The chemical reactions and pathways involving selenocysteine, an essential component of glutathione peroxidase and some other proteins.
GO:0003723 Binding to an RNA molecule or a portion thereof.

Sequence Features

Domain/signature hits from InterPro and related databases.

50 records

Show feature table

Start	End	DB	Term	Name
568	627	Gene3D	G3DSA:1.10.10.10	-
568	627	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
2	352	PANTHER	PTHR43721	ELONGATION FACTOR TU-RELATED
54	64	PRINTS	PR00315	GTP-binding elongation factor signature
54	64	InterPro	IPR000795	Translational (tr)-type GTP-binding domain
2	15	PRINTS	PR00315	GTP-binding elongation factor signature
2	15	InterPro	IPR000795	Translational (tr)-type GTP-binding domain
70	81	PRINTS	PR00315	GTP-binding elongation factor signature
70	81	InterPro	IPR000795	Translational (tr)-type GTP-binding domain
107	116	PRINTS	PR00315	GTP-binding elongation factor signature
107	116	InterPro	IPR000795	Translational (tr)-type GTP-binding domain
2	191	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
2	191	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
266	352	CDD	cd15491	selB_III
2	161	Pfam	PF00009	Elongation factor Tu GTP binding domain
2	161	InterPro	IPR000795	Translational (tr)-type GTP-binding domain
578	626	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
578	626	InterPro	IPR036390	Winged helix DNA-binding domain superfamily
430	497	Gene3D	G3DSA:1.10.10.10	-
430	497	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
583	625	Pfam	PF09107	Elongation factor SelB, winged helix
583	625	InterPro	IPR015191	Translation elongation factor SelB, winged helix, type 3
173	263	Gene3D	G3DSA:2.40.30.10	Translation factors
504	566	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
504	566	InterPro	IPR036390	Winged helix DNA-binding domain superfamily
176	263	FunFam	G3DSA:2.40.30.10:FF:000080	Selenocysteine-specific translation elongation factor
504	565	Gene3D	G3DSA:1.10.10.10	-
504	565	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
269	365	SUPERFAMILY	SSF50465	EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
269	365	InterPro	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal
1	627	NCBIfam	TIGR00475	selenocysteine-specific translation elongation factor
1	627	InterPro	IPR004535	Translation elongation factor, selenocysteine-specific
26	41	ProSitePatterns	PS00301	Translational (tr)-type guanine nucleotide-binding (G) domain signature.
26	41	InterPro	IPR031157	Tr-type G domain, conserved site
2	171	CDD	cd04171	SelB
3	159	NCBIfam	TIGR00231	small GTP-binding protein domain
3	159	InterPro	IPR005225	Small GTP-binding protein domain
172	261	SUPERFAMILY	SSF50447	Translation proteins
172	261	InterPro	IPR009000	Translation protein, beta-barrel domain superfamily
11	173	FunFam	G3DSA:3.40.50.300:FF:001064	Selenocysteine-specific translation elongation factor
529	549	Coils	Coil	Coil
442	497	Pfam	PF09106	Elongation factor SelB, winged helix
442	497	InterPro	IPR015190	Translation elongation factor SelB, winged helix, type 2
432	502	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
432	502	InterPro	IPR036390	Winged helix DNA-binding domain superfamily
568	627	FunFam	G3DSA:1.10.10.10:FF:000350	Selenocysteine-specific translation elongation factor
1	163	Gene3D	G3DSA:3.40.50.300	-
1	163	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
1	169	ProSiteProfiles	PS51722	Translational (tr)-type guanine nucleotide-binding (G) domain profile.
1	169	InterPro	IPR000795	Translational (tr)-type GTP-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

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 PA4807	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
8				0.559
3				0.336

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
5GP	4AC9	Q8J307	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…`
DXC	4AC9	Q8J307	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…`
ENX	1OB5	Q01698	702.6 Da LogP 3.60 TPSA 213.9	2 viol.	✓ Clean	`CC/C=C/[C@H]([C@H]([C@@H](CC(=O)[C@H]([C@@H]([C…`
GNP	4ZU9	O67141	522.2 Da LogP -2.76 TPSA 301.9	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…`
SEC	5LZB	P14081	168.1 Da LogP -1.28 TPSA 63.3	✓ Ro5	✓ Clean	`C([C@@H](C(=O)O)N)[SeH]`
Y1	1LVA	Q46455	88.9 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Y+2]`

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
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[…`
ZINC12501413	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC12958448	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC1532555	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC16546189	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC2159505	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
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…`
ZINC3073318	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869963	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869965	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC9334496	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC104869865	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O…`
ZINC34541308	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC35000839	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC45284491	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC80639694	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC8215481	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC12504289	0.836	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
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…`
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@@…`
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…`
ZINC253610610	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]…`
ZINC4081642	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…`
ZINC4081646	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…`
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.