Protein profile

VK055_1251

DNA topoisomerase III

Genome: KpATCC43816

Gene: AIK79874.1 Structure source: AlphaFold + ColabFold UniProt A0A422YRC8

Export view

Amino acids 648

Annotations 9

Features 47

PDB binders 3

Druggability 0.807

Overview

Basic information about this protein and its source genome.

Accession: VK055_1251
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK79874.1
Status: annotated
Amino acids: 648
Structure source: AlphaFold + ColabFold

5.6.2.1

GO:0006265 The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number. GO:0003917 Catalysis of a DNA topological transformation by transiently cleaving one DNA strand at a time to allow passage of another strand; changes the linking number by +1 per catalytic cycle. GO:0003916 Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0043597 The Y-shaped region of a cytoplasmic replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes. GO:0000287 Binding to a magnesium (Mg) ion.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 21.809
Human E-value: 1.12e-23
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 89.515
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 93.67

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 0.807

Structure A0A422YRC8

Pocket Pocket 4

P2Rank 0.666

Structure A0A422YRC8

Pocket Pocket 1

ColabFold model

FPocket 0.92 · Pocket 1

P2Rank 0.712 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 140 / 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 8 GO

Enzyme Commission (EC)

5.6.2.1

Gene Ontology (GO)

GO:0006265 The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.
GO:0003917 Catalysis of a DNA topological transformation by transiently cleaving one DNA strand at a time to allow passage of another strand; changes the linking number by +1 per catalytic cycle.
GO:0003916 Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0043597 The Y-shaped region of a cytoplasmic replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes.
GO:0000287 Binding to a magnesium (Mg) ion.
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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

47 records

Show feature table

Start	End	DB	Term	Name
128	223	SMART	SM00436	topIban2
128	223	InterPro	IPR003601	DNA topoisomerase, type IA, domain 2
2	607	PANTHER	PTHR11390	PROKARYOTIC DNA TOPOISOMERASE
2	607	InterPro	IPR000380	DNA topoisomerase, type IA
1	156	Gene3D	G3DSA:3.40.50.140	-
158	593	Pfam	PF01131	DNA topoisomerase
158	593	InterPro	IPR013497	DNA topoisomerase, type IA, central
3	135	Pfam	PF01751	Toprim domain
3	135	InterPro	IPR006171	TOPRIM domain
1	627	NCBIfam	TIGR01056	DNA topoisomerase III
1	627	InterPro	IPR005738	DNA topoisomerase III
1	124	SMART	SM00493	toprim5
1	124	InterPro	IPR006171	TOPRIM domain
280	558	SMART	SM00437	topIaneu2
280	558	InterPro	IPR003602	DNA topoisomerase, type IA, DNA-binding domain
290	416	Gene3D	G3DSA:1.10.290.10	Topoisomerase I, domain 4
290	416	InterPro	IPR013826	DNA topoisomerase, type IA, central region, subdomain 3
1	156	FunFam	G3DSA:3.40.50.140:FF:000004	DNA topoisomerase 3
157	603	CDD	cd00186	TOP1Ac
157	603	InterPro	IPR013497	DNA topoisomerase, type IA, central
162	593	Gene3D	G3DSA:1.10.460.10	Topoisomerase I, domain 2
162	593	InterPro	IPR013824	DNA topoisomerase, type IA, central region, subdomain 1
1	134	ProSiteProfiles	PS50880	Toprim domain profile.
1	134	InterPro	IPR006171	TOPRIM domain
217	488	Gene3D	G3DSA:2.70.20.10	Topoisomerase I, domain 3
217	488	InterPro	IPR013825	DNA topoisomerase, type IA, central region, subdomain 2
620	648	MobiDBLite	mobidb-lite	consensus disorder prediction
475	593	FunFam	G3DSA:1.10.460.10:FF:000004	DNA topoisomerase 3
1	149	CDD	cd03362	TOPRIM_TopoIA_TopoIII
1	149	InterPro	IPR034144	DNA topoisomerase 3-like, TOPRIM domain
402	418	PRINTS	PR00417	Prokaryotic DNA topoisomerase I signature
402	418	InterPro	IPR013497	DNA topoisomerase, type IA, central
323	332	PRINTS	PR00417	Prokaryotic DNA topoisomerase I signature
323	332	InterPro	IPR013497	DNA topoisomerase, type IA, central
193	211	PRINTS	PR00417	Prokaryotic DNA topoisomerase I signature
193	211	InterPro	IPR013497	DNA topoisomerase, type IA, central
521	535	PRINTS	PR00417	Prokaryotic DNA topoisomerase I signature
521	535	InterPro	IPR013497	DNA topoisomerase, type IA, central
98	111	PRINTS	PR00417	Prokaryotic DNA topoisomerase I signature
98	111	InterPro	IPR013497	DNA topoisomerase, type IA, central
1	607	SUPERFAMILY	SSF56712	Prokaryotic type I DNA topoisomerase
1	607	InterPro	IPR023405	DNA topoisomerase, type IA, core domain
1	643	Hamap	MF_00953	DNA topoisomerase 3 [topB].
1	643	InterPro	IPR005738	DNA topoisomerase III
290	416	FunFam	G3DSA:1.10.290.10:FF:000004	DNA topoisomerase 3
317	332	ProSitePatterns	PS00396	Prokaryotic DNA topoisomerase I active site.
317	332	InterPro	IPR023406	DNA topoisomerase, type IA, active site

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...

Legend High Medium Low

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_A0A422YRC8	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_1251	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
4				0.807

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	9.37	0.503
2	9.02	0.483
3	2.68	0.079
4	1.81	0.034
5	1.69	0.029

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				0.92
3				0.356

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	8.96	0.48
2	8.14	0.433
3	2.49	0.069
4	2.42	0.065
5	2.07	0.047

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.

53 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
A3P	1CY0	P06612	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
T3P	1CY8	P06612	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)OP(…`
THP	1CY1	P06612	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
ZINC12501123	1.000	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC4228234	1.000	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC6521315	1.000	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…`
ZINC79671662	1.000	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC79671663	1.000	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC3871401	0.887	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3871402	0.887	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3871403	0.887	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3871404	0.887	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC4096223	0.887	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC12958381	0.846	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](OP(=O)(O)…`
ZINC13546985	0.846	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](OP(=O)(O)O…`
ZINC1631259	0.846	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](OP(=O)(O)…`
ZINC79090744	0.846	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](OP(=O)(O)O…`
ZINC13518964	0.827	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.827	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.827	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.827	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.827	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.827	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.827	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.827	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.827	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.827	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.827	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.827	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.827	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC11422512	0.820	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)…`
ZINC13424932	0.750	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1…`
ZINC13424933	0.750	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@@H]1O…`
ZINC2036187	0.750	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]1OP…`
ZINC3861741	0.750	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O…`
ZINC44960119	0.750	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1O…`
ZINC4513863	0.750	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H]1…`
ZINC4513866	0.750	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC14766830	0.725	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	0.725	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	0.725	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	0.725	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	0.725	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	0.725	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	0.725	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…`
ZINC1842580	0.723	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC2159	0.723	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC2545102	0.723	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC25672	0.723	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC2572653	0.723	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)[nH]c1…`
ZINC3831529	0.723	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC5765078	0.723	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC6072455	0.723	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](CO)O2)c(=O)[nH]c1=O`

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.