Protein profile

PA4964

DNA topoisomerase IV subunit A

Genome: NC_002516.2

Gene: parC PA4964 Structure source: AlphaFold UniProt Q9HUK1
Amino acids 754
Annotations 13
Features 28
PDB binders 21
Druggability 0.94

Overview

Basic information about this protein and its source genome.

Accession
PA4964
Gene
parC PA4964
Status
annotated
Amino acids
754
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
28.0
Human E-value
1.91e-09
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

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 0.94
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 12 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

12
  • GO:0005694 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0009340 A heterodimeric enzyme, which in most bacterial species is composed of two subunits, ParC and ParE. Functions in chromosome segregation and can relax supercoiled DNA.
  • GO:0009330 Complex that possesses DNA topoisomerase II (double strand cut, ATP-hydrolyzing) activity.
  • GO:0019897 The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0003918 Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined, driven by ATP hydrolysis. The enzyme changes the linking number in multiples of 2.
  • GO:0007059 The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
  • 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: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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
373 458 Gene3D G3DSA:1.10.268.10 Topoisomerase, domain 3
373 458 InterPro IPR013757 DNA topoisomerase, type IIA, alpha-helical domain superfamily
498 748 FunFam G3DSA:2.120.10.90:FF:000003 DNA topoisomerase 4 subunit A
34 474 CDD cd00187 TOP4c
34 474 InterPro IPR002205 DNA topoisomerase, type IIA, domain A
15 465 SMART SM00434 topIV4
15 465 InterPro IPR002205 DNA topoisomerase, type IIA, domain A
35 487 SUPERFAMILY SSF56719 Type II DNA topoisomerase
35 487 InterPro IPR013760 DNA topoisomerase, type IIA-like domain superfamily
12 745 NCBIfam TIGR01062 DNA topoisomerase IV subunit A
501 750 SUPERFAMILY SSF101904 GyrA/ParC C-terminal domain-like
501 750 InterPro IPR035516 DNA gyrase/topoisomerase IV, subunit A, C-terminal
242 335 FunFam G3DSA:3.30.1360.40:FF:000005 DNA topoisomerase 4 subunit A
8 715 PANTHER PTHR43493 DNA GYRASE/TOPOISOMERASE SUBUNIT A
242 335 Gene3D G3DSA:3.30.1360.40 -
36 472 Pfam PF00521 DNA gyrase/topoisomerase IV, subunit A
36 472 InterPro IPR002205 DNA topoisomerase, type IIA, domain A
498 749 Gene3D G3DSA:2.120.10.90 -
498 749 InterPro IPR035516 DNA gyrase/topoisomerase IV, subunit A, C-terminal
649 689 Pfam PF03989 DNA gyrase C-terminal domain, beta-propeller
649 689 InterPro IPR006691 DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat
602 643 Pfam PF03989 DNA gyrase C-terminal domain, beta-propeller
602 643 InterPro IPR006691 DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat
8 747 Hamap MF_00936 DNA topoisomerase 4 subunit A [parC].
8 747 InterPro IPR005742 DNA topoisomerase IV, subunit A, Gram-negative
36 487 Gene3D G3DSA:3.90.199.10 Topoisomerase II, domain 5
36 487 InterPro IPR013758 DNA topoisomerase, type IIA, domain A, alpha-beta
364 459 FunFam G3DSA:1.10.268.10:FF:000001 DNA gyrase subunit A

3D Structure

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

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Structural evidence

0 + 1

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA4964
AlphaFold full sequence Viewing
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
9 0.506
2 0.265
6 0.247

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.

79 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
31N P20831 509.5 Da LogP 2.28 TPSA 127.7 1 viol. ✓ Clean COc1ccc2c(n1)c(c(cn2)F)C[C@@H](C34CCC(CC3)(CO4)…
50M Q99XG5 374.4 Da LogP 1.33 TPSA 134.4 ✓ Ro5 ✓ Clean C[C@@H]1CN2c3ccc(cc3C[C@]4([C@H]2[C@@H](O1)C)C(…
6EJ Q99XG5 451.5 Da LogP 2.05 TPSA 81.5 ✓ Ro5 ✓ Clean c1cc(c2c3c1C=CC(=O)N3C[C@H]2CN4CCC(CC4)NCc5cc6c…
94H Q99XG5 362.5 Da LogP 3.72 TPSA 83.8 ✓ Ro5 ✓ Clean c1ccc(cc1)[C@H](CN)NC(=O)c2cc(cs2)c3c[nH]c4c3cc…
94K Q99XG5 370.9 Da LogP 4.81 TPSA 55.1 ✓ Ro5 ✓ Clean Cc1c(cc(s1)c2ccccc2Cl)C(=O)N[C@@H](CN)c3ccccc3
9JN Q99XG5 362.5 Da LogP 3.72 TPSA 83.8 ✓ Ro5 ✓ Clean c1ccc(cc1)[C@@H](CN)NC(=O)c2cc(cs2)c3c[nH]c4c3c…
AE8 Q99XG5 467.5 Da LogP 1.16 TPSA 101.7 ✓ Ro5 ✓ Clean c1c(ncc2c1OCCO2)CNC3CCN(CC3)C[C@@]4(CN5c6c4c(cn…
CPF Q99XG5 331.3 Da LogP 1.58 TPSA 74.6 ✓ Ro5 ✓ Clean c1c2c(cc(c1F)N3CCNCC3)N(C=C(C2=O)C(=O)O)C4CC4
DG Q99XG5 347.2 Da LogP -1.54 TPSA 185.8 ✓ Ro5 ✓ Clean c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N…
DT Q99XG5 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)COP(=O…
DU5 Q99XG5 374.5 Da LogP 3.18 TPSA 48.5 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)NCCCN2CCN(CC2)c3c4ccccc4ccn3
E32 Q99XG5 327.4 Da LogP 1.66 TPSA 68.6 ✓ Ro5 ✓ Clean c1cn-2c(n1)C(=O)N(c3c2cc(c(c3)N4CC[C@@H](C4)N)F…
E3E Q99XG5 320.3 Da LogP 3.19 TPSA 52.2 ✓ Ro5 ✓ Clean c1cnccc1c2cc3c(cc2F)-n4ccnc4C(=O)N3C5CC5
EVP Q99XG5 588.6 Da LogP 1.34 TPSA 160.8 2 viol. ✓ Clean C[C@@H]1OC[C@@H]2[C@@H](O1)[C@@H]([C@H]([C@@H](…
JHN Q99XG5 448.5 Da LogP 1.09 TPSA 94.3 ✓ Ro5 ✓ Clean c1c2c(cnc1CNC3CCN(CC3)C[C@@H]4CN5C(=O)C=CC6=C5N…
JK8 Q99XG5 364.8 Da LogP 5.23 TPSA 61.3 1 viol. ✓ Clean c1ccc(cc1)[C@H](CN)Oc2c3cc(ccc3on2)c4ccccc4Cl
MFX B0VP98 401.4 Da LogP 2.37 TPSA 83.8 ✓ Ro5 ✓ Clean COc1c2c(cc(c1N3C[C@@H]4CCCN[C@@H]4C3)F)C(=O)C(=…
Q52 P20831 410.9 Da LogP 4.09 TPSA 50.3 ✓ Ro5 ✓ Clean COc1ccc2c(n1)c(ccn2)CCN3CCC(CC3)NCc4ccc(cc4)Cl
RXV Q99XG5 461.6 Da LogP 3.75 TPSA 83.3 ✓ Ro5 ✓ Clean COc1ccc2c(c1)c(c(cn2)C#N)CCN3CCC(CC3)NCc4cc5c(c…
TNJ B5XU60 360.4 Da LogP 1.92 TPSA 77.3 ✓ Ro5 ✓ Clean Cc1c2c(cc(c1N3C[C@H]4C[C@]4(C3)N)F)C(=C(C(=O)N2…
WCP P20831 507.5 Da LogP 1.72 TPSA 127.6 1 viol. ✓ Clean c1cc2c(nc1CNC34CCC(CC3)(OC4)C[C@@]5(CN6c7c5c(cn…

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.