KpKP13 Protein target profile

Nuclease sbcCD subunit D

Accession: KP13_02076

Gene: sbcD AHE46079.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GJ04

Export view

Length 401

Pocket druggability (P2Rank · AlphaFold DB model) 0.063

Direct ligand evidence 0 57 total records

Functional annotation 0 EC 6 GO

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target: No hit
Gut microbiome similarity: 2.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 91.61 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.063

Structure A0A0H3GJ04

Pocket Pocket 1

Druggability (FPocket) 0.691

Structure A0A0H3GJ04

Pocket Pocket 5

ColabFold model

P2Rank 0.06 · Pocket 1

FPocket 0.594 · Pocket 4

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 109 / 4744 genomes with a hit

Prevalence 2.3%

Sequence

Primary amino-acid sequence viewer.

MRLLHTSDWHLGQNFYSKSRAAEHDAFLTWLLDRAQEHEVDAIIVAGDIFDTGSPPSYARELYNRFVVQLQQTGCRLVVLAGNHDSVAMLNESRDILAFLHTTVVANAGYAPIELPLRDGTPGAIFCPVPFLRPRELVTSQAGHSGREKQQLLLHAISDYYQEQYQQACALRGDRPLPIIASGHLTTVGASKSDAVRDIYIGTLDAFPAQHFPPADYITLGHIHRAQMVGGCEHIRYSGSPLPLSFDETGKAKSVHLVSFSEGRLSAVETLEVPVTQPLAVIKGDLAAITAQLEQWRGVEQDPPVWLDIEITTEDYLHDIQRHIQALTEDLPVEVLLVRRSREQREKILLNAQRETLSELKVEEVFERRLALTEIDEMKRARLHELFAHTVHTLTAEDENT

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks.
GO:0006259 Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0008408 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
GO:0006310 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
1	225	Pfam	PF00149	Calcineurin-like phosphoesterase
1	225	InterPro	IPR004843	Calcineurin-like phosphoesterase domain, ApaH type
276	372	Pfam	PF12320	Type 5 capsule protein repressor C-terminal domain
276	372	InterPro	IPR026843	Nuclease SbcCD subunit D, C-terminal domain
277	340	Gene3D	G3DSA:3.30.160.720	-
1	335	SUPERFAMILY	SSF56300	Metallo-dependent phosphatases
1	335	InterPro	IPR029052	Metallo-dependent phosphatase-like
2	247	CDD	cd00840	MPP_Mre11_N
2	247	InterPro	IPR041796	Mre11 nuclease, N-terminal metallophosphatase domain
1	276	Gene3D	G3DSA:3.60.21.10	-
1	276	InterPro	IPR029052	Metallo-dependent phosphatase-like
1	395	PANTHER	PTHR30337	COMPONENT OF ATP-DEPENDENT DSDNA EXONUCLEASE
1	253	NCBIfam	TIGR00619	exonuclease subunit SbcD
1	253	InterPro	IPR004593	Nuclease SbcCD subunit D

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

Pocket score High Medium Low

How colors and pocket overlays are used

Uniform protein color marks the displayed model as a single molecular object.

Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.

Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.

'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.

'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.

'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.

Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.063

Show in viewer

Surrounding area

Pocket 2 P2Rank #2

0.037

Show in viewer

Surrounding area

Pocket 3 P2Rank #3

0.027

Show in viewer

Surrounding area

Pocket 4 P2Rank #4

0.003

Show in viewer

Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #5

0.691

Show in viewer

Surrounding area

All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold DB AF_A0A0H3GJ04	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_02076	ColabFold	—	—	full sequence	—	Loaded

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.

57 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 7 records from similar proteins

Structural ligands 7 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

2PK PDB via homolog 220.3 Da · LogP 1.53 · TPSA 73.2 Open detail RCSB PDB

2PV PDB via homolog Detail RCSB PDB

2PW PDB via homolog Detail RCSB PDB

2Q0 PDB via homolog Detail RCSB PDB

BU7 PDB via homolog Detail RCSB PDB

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, 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
2PK RCSB PDB	4O4K	Q9X1X0	220.3 Da LogP 1.53 TPSA 73.2	✓ Ro5	✓ Clean	`[H]/N=C\1/NC(=O)/C(=C\c2ccc(cc2)O)/S1`
2PV RCSB PDB	4O5G	Q9X1X0	219.3 Da LogP 1.41 TPSA 79.0	✓ Ro5	✓ Clean	`[H]/N=C\1/NC(=O)/C(=C\c2ccc(cc2)N)/S1`
2PW RCSB PDB	4O43	Q9X1X0	293.4 Da LogP 3.39 TPSA 40.5	✓ Ro5	Alert	`CC[C@@H](C)N1C(=O)/C(=C\c2ccc(cc2)O)/SC1=S`
2Q0 RCSB PDB	4O24	Q9X1X0	293.4 Da LogP 3.25 TPSA 40.5	✓ Ro5	Alert	`CC(C)CN1C(=O)/C(=C/c2ccc(cc2)O)/SC1=S`
BU7 RCSB PDB	6ASC	Q9X1X0	293.4 Da LogP 3.39 TPSA 40.5	✓ Ro5	Alert	`CCCCN1C(=O)/C(=C\c2ccc(cc2)O)/SC1=S`
UKV RCSB PDB	6X1Y	Q9X1X0	251.3 Da LogP 2.18 TPSA 38.3	✓ Ro5	Alert	`COc1cccc(c1)/C=C\2/C(=O)NC(=S)S2`
UL1 RCSB PDB	6X1Z	Q9X1X0	281.4 Da LogP 2.19 TPSA 47.6	✓ Ro5	Alert	`COc1ccc(cc1OC)/C=C\2/C(=O)NC(=S)S2`

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
ZINC2293110020 ZINC	1.000	293.4 Da LogP 3.25 TPSA 40.5	✓ Ro5	Alert	`CC(C)CN1C(=O)C(=Cc2ccc(O)cc2)SC1=S`
ZINC2672553 ZINC	1.000	293.4 Da LogP 3.39 TPSA 40.5	✓ Ro5	Alert	`CCCCN1C(=O)/C(=C/c2ccc(O)cc2)SC1=S`
ZINC2707200 ZINC	1.000	293.4 Da LogP 3.25 TPSA 40.5	✓ Ro5	Alert	`CC(C)CN1C(=O)/C(=C/c2ccc(O)cc2)SC1=S`
ZINC4815953 ZINC	1.000	293.4 Da LogP 3.39 TPSA 40.5	✓ Ro5	Alert	`CCCCN1C(=O)/C(=C\c2ccc(O)cc2)SC1=S`
ZINC5497857 ZINC	1.000	293.4 Da LogP 3.25 TPSA 40.5	✓ Ro5	Alert	`CC(C)CN1C(=O)/C(=C\c2ccc(O)cc2)SC1=S`
ZINC2572998 ZINC	0.925	307.4 Da LogP 3.78 TPSA 40.5	✓ Ro5	Alert	`CCCCCN1C(=O)/C(=C/c2ccc(O)cc2)SC1=S`
ZINC2666879 ZINC	0.902	321.5 Da LogP 4.17 TPSA 40.5	✓ Ro5	Alert	`CCCCCCN1C(=O)/C(=C/c2ccc(O)cc2)SC1=S`
ZINC5502031 ZINC	0.902	321.5 Da LogP 4.17 TPSA 40.5	✓ Ro5	Alert	`CCCCCCN1C(=O)/C(=C\c2ccc(O)cc2)SC1=S`
ZINC1162232 ZINC	0.872	279.4 Da LogP 3.00 TPSA 40.5	✓ Ro5	Alert	`CCCN1C(=O)/C(=C/c2ccc(O)cc2)SC1=S`
ZINC13940186 ZINC	0.841	387.5 Da LogP 3.64 TPSA 56.8	✓ Ro5	Alert	`COc1cccc(OCCOc2cccc(/C=C3\SC(=S)NC3=O)c2)c1`
ZINC2961441 ZINC	0.841	387.5 Da LogP 3.64 TPSA 56.8	✓ Ro5	Alert	`COc1cccc(OCCOc2cccc(/C=C3/SC(=S)NC3=O)c2)c1`
ZINC2873978 ZINC	0.822	401.5 Da LogP 4.03 TPSA 56.8	✓ Ro5	Alert	`COc1cccc(OCCCOc2cccc(/C=C3/SC(=S)NC3=O)c2)c1`
ZINC12600413 ZINC	0.814	309.4 Da LogP 2.97 TPSA 47.6	✓ Ro5	Alert	`COc1cc(/C=C2\SC(=S)NC2=O)ccc1OC(C)C`
ZINC12690557 ZINC	0.814	295.4 Da LogP 2.58 TPSA 47.6	✓ Ro5	Alert	`CCOc1cc(/C=C2\SC(=S)NC2=O)ccc1OC`
ZINC13556347 ZINC	0.814	295.4 Da LogP 2.58 TPSA 47.6	✓ Ro5	Alert	`CCOc1ccc(/C=C2\SC(=S)NC2=O)cc1OC`
ZINC2988006 ZINC	0.814	345.4 Da LogP 1.52 TPSA 81.7	✓ Ro5	Alert	`COc1cc(/C=C2/SC(=S)NC2=O)ccc1OS(C)(=O)=O`
ZINC12600066 ZINC	0.805	265.4 Da LogP 2.49 TPSA 38.3	✓ Ro5	Alert	`COc1ccc(/C=C2\SC(=S)NC2=O)cc1C`
ZINC13942008 ZINC	0.800	417.5 Da LogP 3.65 TPSA 66.0	✓ Ro5	Alert	`COc1ccccc1OCCOc1ccc(/C=C2\SC(=S)NC2=O)cc1OC`
ZINC168930704 ZINC	0.800	219.3 Da LogP 1.41 TPSA 79.0	✓ Ro5	✓ Clean	`N=C1NC(=O)/C(=C/c2ccc(N)cc2)S1`
ZINC2038176995 ZINC	0.800	220.3 Da LogP 1.53 TPSA 73.2	✓ Ro5	✓ Clean	`N=C1NC(=O)C(=Cc2ccc(O)cc2)S1`
ZINC4473160 ZINC	0.800	220.3 Da LogP 1.53 TPSA 73.2	✓ Ro5	✓ Clean	`N=C1NC(=O)/C(=C\c2ccc(O)cc2)S1`
ZINC15135173 ZINC	0.795	309.4 Da LogP 2.11 TPSA 64.6	✓ Ro5	Alert	`COc1cc(/C=C2\SC(=S)NC2=O)ccc1OC(C)=O`
ZINC1164392 ZINC	0.791	295.4 Da LogP 3.83 TPSA 20.3	✓ Ro5	Alert	`CC[C@@H](C)N1C(=O)/C(=C/c2ccc(F)cc2)SC1=S`
ZINC1164394 ZINC	0.791	295.4 Da LogP 3.83 TPSA 20.3	✓ Ro5	Alert	`CC[C@H](C)N1C(=O)/C(=C/c2ccc(F)cc2)SC1=S`
ZINC1165147 ZINC	0.791	356.3 Da LogP 4.45 TPSA 20.3	✓ Ro5	Alert	`CC[C@@H](C)N1C(=O)/C(=C/c2ccc(Br)cc2)SC1=S`
ZINC1165149 ZINC	0.791	356.3 Da LogP 4.45 TPSA 20.3	✓ Ro5	Alert	`CC[C@H](C)N1C(=O)/C(=C/c2ccc(Br)cc2)SC1=S`
ZINC1031760 ZINC	0.786	377.2 Da LogP 2.79 TPSA 38.3	✓ Ro5	Alert	`COc1ccc(/C=C2/SC(=S)NC2=O)cc1I`
ZINC1182221 ZINC	0.786	291.4 Da LogP 3.85 TPSA 20.3	✓ Ro5	Alert	`Cc1ccc(/C=C2/SC(=S)N(CC(C)C)C2=O)cc1`
ZINC1182222 ZINC	0.786	291.4 Da LogP 3.85 TPSA 20.3	✓ Ro5	Alert	`Cc1ccc(/C=C2\SC(=S)N(CC(C)C)C2=O)cc1`
ZINC15163070 ZINC	0.786	377.2 Da LogP 2.79 TPSA 38.3	✓ Ro5	Alert	`COc1ccc(/C=C2\SC(=S)NC2=O)cc1I`
ZINC1857623806 ZINC	0.786	267.3 Da LogP 1.89 TPSA 58.6	✓ Ro5	Alert	`COc1cc(C=C2SC(=S)NC2=O)ccc1O`
ZINC2706865 ZINC	0.786	291.4 Da LogP 4.00 TPSA 20.3	✓ Ro5	Alert	`CCCCN1C(=O)/C(=C/c2ccc(C)cc2)SC1=S`
ZINC35042128 ZINC	0.786	277.3 Da LogP 3.23 TPSA 57.6	✓ Ro5	✓ Clean	`CCCCN1C(=O)S/C(=C/c2ccc(O)cc2)C1=O`
ZINC5503600 ZINC	0.786	291.4 Da LogP 4.00 TPSA 20.3	✓ Ro5	Alert	`CCCCN1C(=O)/C(=C\c2ccc(C)cc2)SC1=S`
ZINC5552373 ZINC	0.786	277.3 Da LogP 3.23 TPSA 57.6	✓ Ro5	✓ Clean	`CCCCN1C(=O)S/C(=C\c2ccc(O)cc2)C1=O`
ZINC15857056 ZINC	0.783	431.5 Da LogP 4.04 TPSA 66.0	✓ Ro5	Alert	`COc1ccccc1OCCCOc1ccc(/C=C2/SC(=S)NC2=O)cc1OC`
ZINC5102380 ZINC	0.783	387.5 Da LogP 3.64 TPSA 56.8	✓ Ro5	Alert	`COc1ccc(OCCOc2cccc(/C=C3\SC(=S)NC3=O)c2)cc1`
ZINC1233033 ZINC	0.780	265.4 Da LogP 2.61 TPSA 40.5	✓ Ro5	Alert	`CCN1C(=O)/C(=C/c2ccc(O)cc2)SC1=S`
ZINC4477965 ZINC	0.780	265.4 Da LogP 2.61 TPSA 40.5	✓ Ro5	Alert	`CCN1C(=O)/C(=C\c2ccc(O)cc2)SC1=S`
ZINC13563168 ZINC	0.778	309.4 Da LogP 2.97 TPSA 47.6	✓ Ro5	Alert	`CCCOc1ccc(/C=C2\SC(=S)NC2=O)cc1OC`
ZINC5128453 ZINC	0.778	309.4 Da LogP 2.97 TPSA 47.6	✓ Ro5	Alert	`CCCOc1cc(/C=C2\SC(=S)NC2=O)ccc1OC`
ZINC12529699 ZINC	0.769	265.3 Da LogP 2.03 TPSA 64.6	✓ Ro5	✓ Clean	`COc1ccc(/C=C2\SC(=O)NC2=O)cc1OC`
ZINC1857622548 ZINC	0.769	265.3 Da LogP 2.03 TPSA 64.6	✓ Ro5	✓ Clean	`COc1ccc(C=C2SC(=O)NC2=O)cc1OC`
ZINC9331564 ZINC	0.769	265.3 Da LogP 2.03 TPSA 64.6	✓ Ro5	✓ Clean	`COc1ccc(/C=C2/SC(=O)NC2=O)cc1OC`
ZINC1117323 ZINC	0.767	311.9 Da LogP 4.20 TPSA 20.3	✓ Ro5	Alert	`CC(C)CN1C(=O)/C(=C/c2ccc(Cl)cc2)SC1=S`
ZINC1446656 ZINC	0.767	319.5 Da LogP 4.67 TPSA 20.3	✓ Ro5	Alert	`CC(C)CN1C(=O)/C(=C/c2ccc(C(C)C)cc2)SC1=S`
ZINC2706848 ZINC	0.767	295.4 Da LogP 3.83 TPSA 20.3	✓ Ro5	Alert	`CCCCN1C(=O)/C(=C/c2ccc(F)cc2)SC1=S`
ZINC4690374 ZINC	0.767	356.3 Da LogP 4.45 TPSA 20.3	✓ Ro5	Alert	`CCCCN1C(=O)/C(=C/c2ccc(Br)cc2)SC1=S`
ZINC4955214 ZINC	0.767	311.9 Da LogP 4.34 TPSA 20.3	✓ Ro5	Alert	`CCCCN1C(=O)/C(=C\c2ccc(Cl)cc2)SC1=S`
ZINC5497852 ZINC	0.767	319.5 Da LogP 4.67 TPSA 20.3	✓ Ro5	Alert	`CC(C)CN1C(=O)/C(=C\c2ccc(C(C)C)cc2)SC1=S`

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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GJ04