Protein profile

VK055_1182

DNA topoisomerase I

Genome: KpATCC43816

Gene: topA AIK79805.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GND2

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Amino acids 865

Annotations 7

Features 65

PDB binders 3

Druggability 0.401

Overview

Basic information about this protein and its source genome.

Accession: VK055_1182
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: topA AIK79805.1
Status: annotated
Amino acids: 865
Structure source: AlphaFold + ColabFold

5.6.2.1

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: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:0005694 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0008270 Binding to a zinc ion (Zn).

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 27.062
Human E-value: 4.26e-30
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 92.948
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 90.42

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 0.401

Structure A0A0H3GND2

Pocket Pocket 54

P2Rank 0.507

Structure A0A0H3GND2

Pocket Pocket 1

ColabFold model

FPocket 0.261 · Pocket 15

P2Rank 0.842 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 168 / 4744 genomes with a hit

Normalized 0.035

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

5.6.2.1

Gene Ontology (GO)

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: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:0005694 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0008270 Binding to a zinc ion (Zn).

Sequence Features

Domain/signature hits from InterPro and related databases.

65 records

Show feature table

Start	End	DB	Term	Name
280	404	Gene3D	G3DSA:1.10.290.10	Topoisomerase I, domain 4
280	404	InterPro	IPR013826	DNA topoisomerase, type IA, central region, subdomain 3
272	527	SMART	SM00437	topIaneu2
272	527	InterPro	IPR003602	DNA topoisomerase, type IA, DNA-binding domain
159	571	CDD	cd00186	TOP1Ac
159	571	InterPro	IPR013497	DNA topoisomerase, type IA, central
3	132	SMART	SM00493	toprim5
3	132	InterPro	IPR006171	TOPRIM domain
133	221	SMART	SM00436	topIban2
133	221	InterPro	IPR003601	DNA topoisomerase, type IA, domain 2
1	163	Gene3D	G3DSA:3.40.50.140	-
2	837	PANTHER	PTHR42785	DNA TOPOISOMERASE, TYPE IA, CORE
2	837	InterPro	IPR000380	DNA topoisomerase, type IA
3	154	CDD	cd03363	TOPRIM_TopoIA_TopoI
3	154	InterPro	IPR034149	DNA topoisomerase 1, TOPRIM domain
3	609	SUPERFAMILY	SSF56712	Prokaryotic type I DNA topoisomerase
3	609	InterPro	IPR023405	DNA topoisomerase, type IA, core domain
702	743	SUPERFAMILY	SSF57783	Zinc beta-ribbon
5	635	NCBIfam	TIGR01051	type I DNA topoisomerase
5	635	InterPro	IPR005733	DNA topoisomerase I, bacterial-type
213	473	Gene3D	G3DSA:2.70.20.10	Topoisomerase I, domain 3
213	473	InterPro	IPR013825	DNA topoisomerase, type IA, central region, subdomain 2
808	865	FunFam	G3DSA:2.20.25.10:FF:000013	DNA topoisomerase 1
703	744	FunFam	G3DSA:3.30.65.10:FF:000003	DNA topoisomerase 1
157	564	Pfam	PF01131	DNA topoisomerase
157	564	InterPro	IPR013497	DNA topoisomerase, type IA, central
5	142	Pfam	PF01751	Toprim domain
5	142	InterPro	IPR006171	TOPRIM domain
597	622	Pfam	PF01396	Topoisomerase DNA binding C4 zinc finger
597	622	InterPro	IPR013498	DNA topoisomerase, type IA, zn finger
708	745	Pfam	PF01396	Topoisomerase DNA binding C4 zinc finger
708	745	InterPro	IPR013498	DNA topoisomerase, type IA, zn finger
583	643	Gene3D	G3DSA:3.30.65.10	Bacterial Topoisomerase I, domain 1
745	807	Gene3D	G3DSA:3.30.65.10	Bacterial Topoisomerase I, domain 1
702	744	Gene3D	G3DSA:3.30.65.10	Bacterial Topoisomerase I, domain 1
808	865	Gene3D	G3DSA:2.20.25.10	-
1	163	FunFam	G3DSA:3.40.50.140:FF:000001	DNA topoisomerase 1
744	807	SUPERFAMILY	SSF57783	Zinc beta-ribbon
758	793	Pfam	PF08272	Topoisomerase I zinc-ribbon-like
758	793	InterPro	IPR013263	DNA topoisomerase I, zinc ribbon-like, bacterial-type
824	862	Pfam	PF08272	Topoisomerase I zinc-ribbon-like
824	862	InterPro	IPR013263	DNA topoisomerase I, zinc ribbon-like, bacterial-type
164	571	Gene3D	G3DSA:1.10.460.10	Topoisomerase I, domain 2
164	571	InterPro	IPR013824	DNA topoisomerase, type IA, central region, subdomain 1
584	643	FunFam	G3DSA:3.30.65.10:FF:000002	DNA topoisomerase 1
280	404	FunFam	G3DSA:1.10.290.10:FF:000002	DNA topoisomerase 1
37	63	MobiDBLite	mobidb-lite	consensus disorder prediction
3	732	Hamap	MF_00952	DNA topoisomerase 1 [topA].
3	732	InterPro	IPR028612	DNA topoisomerase I, type IA
3	142	ProSiteProfiles	PS50880	Toprim domain profile.
3	142	InterPro	IPR006171	TOPRIM domain
745	807	FunFam	G3DSA:3.30.65.10:FF:000001	DNA topoisomerase 1
314	323	PRINTS	PR00417	Prokaryotic DNA topoisomerase I signature
314	323	InterPro	IPR013497	DNA topoisomerase, type IA, central
106	119	PRINTS	PR00417	Prokaryotic DNA topoisomerase I signature
106	119	InterPro	IPR013497	DNA topoisomerase, type IA, central
490	504	PRINTS	PR00417	Prokaryotic DNA topoisomerase I signature
490	504	InterPro	IPR013497	DNA topoisomerase, type IA, central
390	406	PRINTS	PR00417	Prokaryotic DNA topoisomerase I signature
390	406	InterPro	IPR013497	DNA topoisomerase, type IA, central
191	209	PRINTS	PR00417	Prokaryotic DNA topoisomerase I signature
191	209	InterPro	IPR013497	DNA topoisomerase, type IA, central
309	323	ProSitePatterns	PS00396	Prokaryotic DNA topoisomerase I active site.
309	323	InterPro	IPR023406	DNA topoisomerase, type IA, active site
809	864	SUPERFAMILY	SSF57783	Zinc beta-ribbon

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_A0A0H3GND2	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_1182	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
54				0.401
60				0.184
65				0.003
5				0.0

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	10.99	0.507
2	5.02	0.188
3	4.95	0.184
4	3.39	0.096
5	3.22	0.089

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
70				0.182
69				0.09
62				0.005
71				0.0

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	23.54	0.842
2	4.31	0.147
3	4.17	0.139
4	2.3	0.048
5	2.29	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.