Protein profile

KP13_05420

Exodeoxyribonuclease I

Genome: KpKP13

Gene: sbcB AHE43706.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GSG0

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Amino acids 474

Annotations 8

Features 27

PDB binders 2

Druggability 0.468

Overview

Basic information about this protein and its source genome.

Accession: KP13_05420
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: sbcB AHE43706.1
Status: annotated
Amino acids: 474
Structure source: AlphaFold + ColabFold

3.1.11.1

GO:0000175 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule. GO:0003676 Binding to a nucleic acid. 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 84.534
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 95.92

Selected Druggability evidence

AlphaFold / UniProt model

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 0.468

Structure A0A0H3GSG0

Pocket Pocket 15

P2Rank 0.678

Structure A0A0H3GSG0

Pocket Pocket 1

ColabFold model

FPocket 0.744 · Pocket 1

P2Rank 0.676 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 144 / 4744 genomes with a hit

Normalized 0.03

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:0003676 Binding to a nucleic acid.
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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records

Show feature table

Start	End	DB	Term	Name
13	431	PANTHER	PTHR11046	OLIGORIBONUCLEASE, MITOCHONDRIAL
13	431	InterPro	IPR022894	Oligoribonuclease
358	474	ProSiteProfiles	PS51785	Exonuclease I (ExoI) C-terminal domain profile.
358	474	InterPro	IPR034748	Exonuclease I, C-terminal alpha-helical domain
8	200	FunFam	G3DSA:3.30.420.10:FF:000033	Exodeoxyribonuclease I
12	189	Pfam	PF00929	Exonuclease
12	189	InterPro	IPR013520	Exonuclease, RNase T/DNA polymerase III
359	419	FunFam	G3DSA:1.20.1280.70:FF:000001	Exodeoxyribonuclease I
421	474	Gene3D	G3DSA:1.10.287.1240	-
213	352	Gene3D	G3DSA:3.30.1520.20	Exonuclease ExoI, domain 2
213	352	InterPro	IPR038649	Exonuclease I, SH3-like domain superfamily
9	200	Gene3D	G3DSA:3.30.420.10	-
9	200	InterPro	IPR036397	Ribonuclease H superfamily
439	466	Coils	Coil	Coil
211	471	Pfam	PF08411	Exonuclease C-terminal
211	471	InterPro	IPR013620	Exodeoxyribonuclease I, C-terminal
213	351	FunFam	G3DSA:3.30.1520.20:FF:000001	Exodeoxyribonuclease I
9	473	SUPERFAMILY	SSF53098	Ribonuclease H-like
9	473	InterPro	IPR012337	Ribonuclease H-like superfamily
2	474	PIRSF	PIRSF000977	Exodeoxyribonuclease_I
2	474	InterPro	IPR023607	Exodeoxyribonuclease I
201	354	ProSiteProfiles	PS51784	Exonuclease I (ExoI) SH3-like domain profile.
201	354	InterPro	IPR034747	Exonuclease I, SH3-like domain
11	194	CDD	cd06138	ExoI_N
9	202	SMART	SM00479	exoiiiendus
9	202	InterPro	IPR013520	Exonuclease, RNase T/DNA polymerase III
358	419	Gene3D	G3DSA:1.20.1280.70	Exonuclease ExoI, domain 3

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 2

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GSG0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05420	ColabFold	—	—	full sequence	—	Loaded

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				0.031
21				0.005
33				0.004
4				0.002

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	15.65	0.678
2	6.54	0.278
3	5.56	0.22
4	4.42	0.154
5	2.2	0.044

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				0.744
5				0.604
21				0.324

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	10.54	0.566
2	5.61	0.269
3	2.96	0.096
4	2.0	0.043
5	1.17	0.01

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.