Protein profile

PA4316

exonuclease I

Genome: NC_002516.2

Gene: PA4316 sbcB Structure source: AlphaFold UniProt Q9HW85

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Amino acids 480

Annotations 8

Features 26

PDB binders 2

Druggability 0.838

Overview

Basic information about this protein and its source genome.

Accession: PA4316
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA4316 sbcB
Status: annotated
Amino acids: 480
Structure source: AlphaFold

3.1.11.1

GO:0000175 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0046872 Binding to a metal ion. GO:0008310 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a single-stranded DNA molecule. GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. GO:0004529 Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of a DNA molecule.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: hit
Essential (DEG): Y
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 0.838

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

3.1.11.1

Gene Ontology (GO)

GO:0000175 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0046872 Binding to a metal ion.
GO:0008310 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a single-stranded DNA molecule.
GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
GO:0004529 Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of a DNA molecule.
GO:0003676 Binding to a nucleic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records

Show feature table

Start	End	DB	Term	Name
5	196	FunFam	G3DSA:3.30.420.10:FF:000033	Exodeoxyribonuclease I
207	470	Pfam	PF08411	Exonuclease C-terminal
207	470	InterPro	IPR013620	Exodeoxyribonuclease I, C-terminal
6	198	SMART	SM00479	exoiiiendus
6	198	InterPro	IPR013520	Exonuclease, RNase T/DNA polymerase III
1	477	PIRSF	PIRSF000977	Exodeoxyribonuclease_I
1	477	InterPro	IPR023607	Exodeoxyribonuclease I
209	348	Gene3D	G3DSA:3.30.1520.20	Exonuclease ExoI, domain 2
209	348	InterPro	IPR038649	Exonuclease I, SH3-like domain superfamily
416	473	Gene3D	G3DSA:1.10.287.1240	-
353	473	ProSiteProfiles	PS51785	Exonuclease I (ExoI) C-terminal domain profile.
353	473	InterPro	IPR034748	Exonuclease I, C-terminal alpha-helical domain
354	414	FunFam	G3DSA:1.20.1280.70:FF:000001	Exodeoxyribonuclease I
8	190	CDD	cd06138	ExoI_N
5	196	Gene3D	G3DSA:3.30.420.10	-
5	196	InterPro	IPR036397	Ribonuclease H superfamily
354	413	Gene3D	G3DSA:1.20.1280.70	Exonuclease ExoI, domain 3
209	347	FunFam	G3DSA:3.30.1520.20:FF:000001	Exodeoxyribonuclease I
6	430	PANTHER	PTHR11046	OLIGORIBONUCLEASE, MITOCHONDRIAL
6	430	InterPro	IPR022894	Oligoribonuclease
7	453	SUPERFAMILY	SSF53098	Ribonuclease H-like
7	453	InterPro	IPR012337	Ribonuclease H-like superfamily
9	188	Pfam	PF00929	Exonuclease
9	188	InterPro	IPR013520	Exonuclease, RNase T/DNA polymerase III
197	350	ProSiteProfiles	PS51784	Exonuclease I (ExoI) SH3-like domain profile.
197	350	InterPro	IPR034747	Exonuclease I, SH3-like 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 PA4316	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
6				0.838
1				0.361

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.

52 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
BBP	3HL8	P04995	307.8 Da LogP 4.09 TPSA 45.6	✓ Ro5	✓ Clean	`CC(C)(C)C1=NN(C(=O)C1)c2nc3ccc(cc3s2)Cl`
CF1	3HP9	P04995	345.7 Da LogP 4.81 TPSA 58.6	✓ Ro5	Alert	`COc1ccc(c(c1)C(=O)O)Nc2cc(ccc2Cl)C(F)(F)F`

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
ZINC5283936	0.702	273.4 Da LogP 3.44 TPSA 45.6	✓ Ro5	✓ Clean	`CC(C)(C)C1=NN(c2nc3ccccc3s2)C(=O)C1`
ZINC1579743	0.660	315.7 Da LogP 4.80 TPSA 49.3	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1Nc1cc(C(F)(F)F)ccc1Cl`
ZINC4099443	0.660	277.7 Da LogP 3.79 TPSA 58.6	✓ Ro5	Alert	`COc1ccc(Nc2ccccc2Cl)c(C(=O)O)c1`
ZINC101566	0.600	329.7 Da LogP 4.62 TPSA 38.3	✓ Ro5	✓ Clean	`COc1ccc(C(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1`
ZINC1729836	0.587	273.3 Da LogP 3.15 TPSA 67.8	✓ Ro5	Alert	`COc1ccc(Nc2ccc(OC)cc2C(=O)O)cc1`
ZINC272451	0.566	343.7 Da LogP 4.55 TPSA 38.3	✓ Ro5	✓ Clean	`COc1ccc(CC(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1`
ZINC58157306	0.561	423.8 Da LogP 3.95 TPSA 81.7	✓ Ro5	✓ Clean	`COC(=O)c1cc(OC)ccc1NS(=O)(=O)c1cc(C(F)(F)F)ccc1…`
ZINC437703	0.556	329.7 Da LogP 4.62 TPSA 38.3	✓ Ro5	✓ Clean	`COc1cccc(C(=O)Nc2cc(C(F)(F)F)ccc2Cl)c1`
ZINC6936383	0.556	369.3 Da LogP 3.67 TPSA 84.9	✓ Ro5	✓ Clean	`COc1ccc(C(=O)Nc2cc(C(F)(F)F)ccc2C(=O)O)c(OC)c1`
ZINC2848323	0.545	373.8 Da LogP 4.77 TPSA 47.6	✓ Ro5	✓ Clean	`COc1ccc(O[C@@H](C)C(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1`
ZINC2848324	0.545	373.8 Da LogP 4.77 TPSA 47.6	✓ Ro5	✓ Clean	`COc1ccc(O[C@H](C)C(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1`
ZINC2172100	0.542	253.6 Da LogP 3.54 TPSA 38.3	✓ Ro5	✓ Clean	`COC(=O)Nc1cc(C(F)(F)F)ccc1Cl`
ZINC94596758	0.542	281.2 Da LogP 4.15 TPSA 49.3	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(F)(F)F)ccc1Nc1ccccc1`
ZINC22151790	0.537	316.7 Da LogP 4.20 TPSA 62.2	✓ Ro5	✓ Clean	`O=C(O)c1cccnc1Nc1cc(C(F)(F)F)ccc1Cl`
ZINC481307	0.537	310.3 Da LogP 3.56 TPSA 64.3	✓ Ro5	✓ Clean	`COc1ccc(Nc2cccc(C(F)(F)F)c2)c(C(N)=O)c1`
ZINC1140239	0.536	357.8 Da LogP 4.94 TPSA 38.3	✓ Ro5	✓ Clean	`COc1ccc(CCC(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1`
ZINC13320435	0.536	358.7 Da LogP 4.69 TPSA 50.4	✓ Ro5	✓ Clean	`COc1ccc(CNC(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1`
ZINC753310	0.528	365.8 Da LogP 4.17 TPSA 55.4	✓ Ro5	✓ Clean	`COc1ccc(S(=O)(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1`
ZINC4922336	0.526	358.7 Da LogP 4.91 TPSA 53.8	✓ Ro5	Alert	`COc1ccc(/C(C)=N/Nc2cc(C(F)(F)F)ccc2Cl)c(O)c1`
ZINC13320494	0.525	413.8 Da LogP 4.72 TPSA 44.8	✓ Ro5	Alert	`COc1ccc(N2CCN(C(=O)Nc3cc(C(F)(F)F)ccc3Cl)CC2)cc1`
ZINC56838	0.523	224.6 Da LogP 3.06 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(F)(F)F)ccc1Cl`
ZINC164757	0.520	250.2 Da LogP 2.33 TPSA 55.8	✓ Ro5	✓ Clean	`COc1ccc(OCC(F)(F)F)c(C(=O)O)c1`
ZINC2814773	0.519	343.7 Da LogP 4.31 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)Nc1cc(C(F)(F)F)ccc1Cl`
ZINC683171	0.519	389.8 Da LogP 4.64 TPSA 56.8	✓ Ro5	✓ Clean	`COc1cc(OC)c(C(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1OC`
ZINC13320421	0.517	372.8 Da LogP 4.73 TPSA 50.4	✓ Ro5	✓ Clean	`COc1ccc(CCNC(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1`
ZINC20739021	0.517	382.8 Da LogP 4.96 TPSA 43.3	✓ Ro5	✓ Clean	`COc1ccc2c(ccn2CC(=O)Nc2cc(C(F)(F)F)ccc2Cl)c1`
ZINC13320508	0.516	457.9 Da LogP 4.73 TPSA 54.0	✓ Ro5	✓ Clean	`COc1ccc(OC)c(CN2CCN(C(=O)Nc3cc(C(F)(F)F)ccc3Cl)…`
ZINC12956694	0.511	220.1 Da LogP 2.41 TPSA 46.5	✓ Ro5	✓ Clean	`COc1ccc(C(F)(F)F)cc1C(=O)O`
ZINC134025	0.511	209.2 Da LogP 1.35 TPSA 75.6	✓ Ro5	✓ Clean	`COc1ccc(NC(C)=O)c(C(=O)O)c1`
ZINC20220689	0.511	238.6 Da LogP 3.15 TPSA 26.3	✓ Ro5	✓ Clean	`COC(=O)c1cc(C(F)(F)F)ccc1Cl`
ZINC308840216	0.511	299.5 Da LogP 3.52 TPSA 26.3	✓ Ro5	✓ Clean	`COc1ccc(Cl)c(C(=O)C(F)(F)Br)c1`
ZINC351305	0.511	237.6 Da LogP 3.32 TPSA 29.1	✓ Ro5	✓ Clean	`CC(=O)Nc1cc(C(F)(F)F)ccc1Cl`
ZINC389373086	0.511	238.6 Da LogP 3.09 TPSA 26.3	✓ Ro5	✓ Clean	`COc1ccc(Cl)c(C(=O)C(F)(F)F)c1`
ZINC54527155	0.511	219.2 Da LogP 2.45 TPSA 49.3	✓ Ro5	✓ Clean	`CNc1ccc(C(F)(F)F)cc1C(=O)O`
ZINC72338570	0.511	220.1 Da LogP 2.41 TPSA 46.5	✓ Ro5	✓ Clean	`COc1ccc(C(F)(F)F)c(C(=O)O)c1`
ZINC18044165	0.510	319.6 Da LogP 4.79 TPSA 32.7	✓ Ro5	✓ Clean	`CC(C)(C)C1=NN(c2c(Cl)cc(Cl)cc2Cl)C(=O)C1`
ZINC102646525	0.509	327.8 Da LogP 4.09 TPSA 45.6	✓ Ro5	✓ Clean	`O=C1CC(c2ccc(Cl)cc2)=NN1c1nc2ccccc2s1`
ZINC438360	0.509	329.7 Da LogP 4.62 TPSA 38.3	✓ Ro5	✓ Clean	`COc1ccccc1C(=O)Nc1cc(C(F)(F)F)ccc1Cl`
ZINC712722	0.509	359.7 Da LogP 4.63 TPSA 47.6	✓ Ro5	✓ Clean	`COc1ccc(C(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1OC`
ZINC7791601	0.509	343.7 Da LogP 4.55 TPSA 38.3	✓ Ro5	✓ Clean	`COc1ccc(CC(=O)Nc2ccc(C(F)(F)F)cc2Cl)cc1`
ZINC1182672	0.509	418.8 Da LogP 4.50 TPSA 59.6	✓ Ro5	✓ Clean	`COc1cc(OC)cc(C(=O)NC(=S)Nc2cc(C(F)(F)F)ccc2Cl)c1`
ZINC4922856	0.509	358.7 Da LogP 4.82 TPSA 42.9	✓ Ro5	✓ Clean	`COc1ccc(OC)c(/C=N/Nc2cc(C(F)(F)F)ccc2Cl)c1`
ZINC12697899	0.508	429.8 Da LogP 3.88 TPSA 70.7	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)CN(C)CC(=O)Nc2cc(C(F)(F)F)ccc2Cl)…`
ZINC1148669	0.508	436.8 Da LogP 3.63 TPSA 75.7	✓ Ro5	✓ Clean	`COc1ccc(S(=O)(=O)N(C)CC(=O)Nc2cc(C(F)(F)F)ccc2C…`
ZINC3052213	0.500	422.8 Da LogP 3.80 TPSA 75.7	✓ Ro5	✓ Clean	`CN(C)S(=O)(=O)Oc1ccc(C(=O)Nc2cc(C(F)(F)F)ccc2Cl…`
ZINC308807291	0.500	255.0 Da LogP 3.36 TPSA 26.3	✓ Ro5	✓ Clean	`COc1ccc(Cl)c(C(=O)C(F)(F)Cl)c1`
ZINC346997	0.500	279.8 Da LogP 4.31 TPSA 28.5	✓ Ro5	✓ Clean	`CC1=NN(c2nc3ccc(Cl)cc3s2)C(C)(C)C1`
ZINC4842878	0.500	359.7 Da LogP 4.63 TPSA 47.6	✓ Ro5	✓ Clean	`COc1cc(OC)cc(C(=O)Nc2ccc(C(F)(F)F)cc2Cl)c1`
ZINC6145620	0.500	344.7 Da LogP 4.52 TPSA 53.9	✓ Ro5	Alert	`COc1ccc(O)c(/C=N/Nc2cc(C(F)(F)F)ccc2Cl)c1`
ZINC753351	0.500	359.7 Da LogP 4.63 TPSA 47.6	✓ Ro5	✓ Clean	`COc1cccc(OC)c1C(=O)Nc1cc(C(F)(F)F)ccc1Cl`

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.