Protein profile

KP13_05582

thermonuclease family protein

Genome: KpKP13

Gene: AHE41936.1 Structure source: AlphaFold + ColabFold UniProt S4VF90

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Amino acids 198

Annotations 3

Features 16

PDB binders 1

Druggability 0.292

Overview

Basic information about this protein and its source genome.

Accession: KP13_05582
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE41936.1
Status: annotated
Amino acids: 198
Structure source: AlphaFold + ColabFold

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Unknown
ColabFold pLDDT: 85.62

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 0.292

Structure S4VF90

Pocket Pocket 1

P2Rank 0.563

Structure S4VF90

Pocket Pocket 1

ColabFold model

FPocket 0.039 · Pocket 3

P2Rank 0.588 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 4 / 4744 genomes with a hit

Normalized 0.001

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks.
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
51	183	ProSiteProfiles	PS50830	Thermonuclease domain profile.
51	183	InterPro	IPR016071	Staphylococcal nuclease (SNase-like), OB-fold
88	197	PANTHER	PTHR12302	EBNA2 BINDING PROTEIN P100
21	43	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
46	50	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
47	186	Gene3D	G3DSA:2.40.50.90	-
47	186	InterPro	IPR035437	SNase-like, OB-fold superfamily
1	33	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
51	198	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	50	Phobius	SIGNAL_PEPTIDE	Signal peptide region
34	45	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
51	183	SMART	SM00318	SNASE_2
88	182	Pfam	PF00565	Staphylococcal nuclease homologue
88	182	InterPro	IPR016071	Staphylococcal nuclease (SNase-like), OB-fold
48	184	SUPERFAMILY	SSF50199	Staphylococcal nuclease
48	184	InterPro	IPR035437	SNase-like, OB-fold superfamily

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_S4VF90	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05582	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				0.292

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				7.59	0.401

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				9.34	0.501
2				1.21	0.011

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.

51 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
THP	1JOQ	P00644	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O…`

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
ZINC11422512	1.000	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](OP(=O)(O)O)[C@@H](COP(=O)(O)…`
ZINC6521315	0.820	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](OP(=O)(O)O)[C@@H](CO)O2)c(=O…`
ZINC13523519	0.800	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)O2)c(…`
ZINC1532628	0.800	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=…`
ZINC1678872	0.800	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=O…`
ZINC2047010	0.800	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=O…`
ZINC3870253	0.800	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O…`
ZINC3870254	0.800	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O)…`
ZINC6523446	0.800	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=…`
ZINC12503817	0.690	347.2 Da LogP -0.08 TPSA 179.6	✓ Ro5	Alert	`Cc1cn([C@H]2C[C@H](N=[N+]=[N-])[C@@H](COP(=O)(O…`
ZINC12503053	0.679	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC33979243	0.679	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC33979244	0.679	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)OP(=O)…`
ZINC33979245	0.679	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)OP(=…`
ZINC33979246	0.679	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC8215882	0.679	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC17107637	0.673	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](COP(N)(N)=O)O2)c(…`
ZINC17107641	0.673	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](COP(N)(N)=O)O2)c(=…`
ZINC5493427	0.673	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](COP(N)(N)=O)O2)c(=O…`
ZINC5493430	0.673	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](COP(N)(N)=O)O2)c(=…`
ZINC13507072	0.655	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)O[P@…`
ZINC33979251	0.655	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC13515793	0.636	338.2 Da LogP -2.43 TPSA 171.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@H]2…`
ZINC12503902	0.625	326.2 Da LogP -1.57 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1[nH]c(=O)n([C@@H]2C[C@@H](O)[C@@H](COP(=O)(…`
ZINC1529898	0.625	326.2 Da LogP -1.57 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1[nH]c(=O)n([C@@H]2C[C@@H](O)[C@H](COP(=O)(O…`
ZINC3871118	0.625	326.2 Da LogP -1.57 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1[nH]c(=O)n([C@@H]2C[C@H](O)[C@H](COP(=O)(O)…`
ZINC3875881	0.625	326.2 Da LogP -1.57 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1[nH]c(=O)n([C@H]2C[C@H](O)[C@@H](COP(=O)(O)…`
ZINC6090961	0.625	387.1 Da LogP -0.94 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1[nH]c(=O)n([C@H]2C[C@H](O)[C@@H](COP(=O)(O)…`
ZINC6524115	0.625	326.2 Da LogP -1.57 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1[nH]c(=O)n([C@@H]2C[C@H](O)[C@@H](COP(=O)(O…`
ZINC111459735	0.623	481.2 Da LogP -1.20 TPSA 249.9	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](N)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC1319360	0.621	326.3 Da LogP -0.37 TPSA 116.7	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H]1O[C@H](n2cc(C)c(=O)[nH]c2=O)C[C@…`
ZINC3861762	0.621	326.3 Da LogP -0.37 TPSA 116.7	✓ Ro5	✓ Clean	`CC(=O)OC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C@…`
ZINC43693090	0.621	398.4 Da LogP -1.55 TPSA 150.8	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](OS(C)(=O)=O)[C@H](COS(C)(=O)…`
ZINC4758963	0.621	326.3 Da LogP -0.37 TPSA 116.7	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H]1O[C@H](n2cc(C)c(=O)[nH]c2=O)C[C@…`
ZINC4758964	0.621	326.3 Da LogP -0.37 TPSA 116.7	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C…`
ZINC57124	0.621	326.3 Da LogP -0.37 TPSA 116.7	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C…`
ZINC79125017	0.621	398.4 Da LogP -1.55 TPSA 150.8	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](OS(C)(=O)=O)[C@@H](COS(C)(=O…`
ZINC1727053	0.614	320.3 Da LogP -1.53 TPSA 127.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](OS(C)(=O)=O)[C@H](CO)O2)c(…`
ZINC5085198	0.614	320.3 Da LogP -1.53 TPSA 127.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](OS(C)(=O)=O)[C@H](CO)O2)c(=…`
ZINC5085200	0.614	320.3 Da LogP -1.53 TPSA 127.7	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](OS(C)(=O)=O)[C@H](CO)O2)c(=O…`
ZINC5085203	0.614	320.3 Da LogP -1.53 TPSA 127.7	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](OS(C)(=O)=O)[C@H](CO)O2)c(=…`
ZINC6667024	0.611	256.3 Da LogP -0.86 TPSA 93.5	✓ Ro5	✓ Clean	`COC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C@@H]1O`
ZINC5765073	0.604	241.2 Da LogP -1.55 TPSA 110.3	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CN)O2)c(=O)[nH]c1=O`
ZINC14766830	0.596	284.3 Da LogP -0.94 TPSA 110.6	✓ Ro5	✓ Clean	`CC(=O)O[C@@H]1C[C@@H](n2cc(C)c(=O)[nH]c2=O)O[C@…`
ZINC14766832	0.596	284.3 Da LogP -0.94 TPSA 110.6	✓ Ro5	✓ Clean	`CC(=O)O[C@@H]1C[C@H](n2cc(C)c(=O)[nH]c2=O)O[C@@…`
ZINC2516145	0.596	284.3 Da LogP -0.94 TPSA 110.6	✓ Ro5	✓ Clean	`CC(=O)O[C@@H]1C[C@@H](n2cc(C)c(=O)[nH]c2=O)O[C@…`
ZINC5119363	0.596	284.3 Da LogP -0.94 TPSA 110.6	✓ Ro5	✓ Clean	`CC(=O)O[C@H]1C[C@@H](n2cc(C)c(=O)[nH]c2=O)O[C@H…`
ZINC5119364	0.596	284.3 Da LogP -0.94 TPSA 110.6	✓ Ro5	✓ Clean	`CC(=O)O[C@H]1C[C@H](n2cc(C)c(=O)[nH]c2=O)O[C@H]…`
ZINC5119365	0.596	284.3 Da LogP -0.94 TPSA 110.6	✓ Ro5	✓ Clean	`CC(=O)O[C@@H]1C[C@H](n2cc(C)c(=O)[nH]c2=O)O[C@H…`
ZINC6521309	0.596	284.3 Da LogP -0.94 TPSA 110.6	✓ Ro5	✓ Clean	`CC(=O)O[C@H]1C[C@H](n2cc(C)c(=O)[nH]c2=O)O[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.