Protein profile

PA3168

DNA gyrase subunit A

Genome: NC_002516.2

Gene: gyrA PA3168 Structure source: AlphaFold UniProt P48372
Amino acids 923
Annotations 12
Features 38
PDB binders 24
Druggability 0.62

Overview

Basic information about this protein and its source genome.

Accession
PA3168
Gene
gyrA PA3168
Status
annotated
Amino acids
923
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
25.401
Human E-value
2.93e-14
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 0.62
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

11
  • 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:0009330 Complex that possesses DNA topoisomerase II (double strand cut, ATP-hydrolyzing) activity.
  • 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:0034335 Catalytic introduction of negative supercoils into a DNA molecule or region thereof. In bacteria, negative supercoils are only introduced by DNA gyrase, a type II topoisomerase, but not all DNA gyrases are capable of introducing supercoils. In bacteria, the level of supercoiling varies widely between species and has been characterized properly in only a handful of organisms. The best characterized enzyme, from E.coli, is exceptionally proficient at supercoiling and this ability is not representative of all bacteria.
  • 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:0006261 A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
  • 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: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.

38 records
Show feature table
Start End DB Term Name
32 507 Pfam PF00521 DNA gyrase/topoisomerase IV, subunit A
880 923 MobiDBLite mobidb-lite consensus disorder prediction
30 510 CDD cd00187 TOP4c
30 510 InterPro IPR002205 DNA topoisomerase, type IIA, domain A
30 523 SUPERFAMILY SSF56719 Type II DNA topoisomerase
30 523 InterPro IPR013760 DNA topoisomerase, type IIA-like domain superfamily
236 334 Gene3D G3DSA:3.30.1360.40 -
11 500 SMART SM00434 topIV4
11 500 InterPro IPR002205 DNA topoisomerase, type IIA, domain A
32 251 FunFam G3DSA:3.90.199.10:FF:000001 DNA gyrase subunit A
534 898 SUPERFAMILY SSF101904 GyrA/ParC C-terminal domain-like
534 898 InterPro IPR035516 DNA gyrase/topoisomerase IV, subunit A, C-terminal
4 887 PANTHER PTHR43493 DNA GYRASE/TOPOISOMERASE SUBUNIT A
890 923 MobiDBLite mobidb-lite consensus disorder prediction
500 520 Coils Coil Coil
788 833 Pfam PF03989 DNA gyrase C-terminal domain, beta-propeller
788 833 InterPro IPR006691 DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat
539 586 Pfam PF03989 DNA gyrase C-terminal domain, beta-propeller
539 586 InterPro IPR006691 DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat
689 732 Pfam PF03989 DNA gyrase C-terminal domain, beta-propeller
689 732 InterPro IPR006691 DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat
837 883 Pfam PF03989 DNA gyrase C-terminal domain, beta-propeller
837 883 InterPro IPR006691 DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat
591 638 Pfam PF03989 DNA gyrase C-terminal domain, beta-propeller
591 638 InterPro IPR006691 DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat
737 781 Pfam PF03989 DNA gyrase C-terminal domain, beta-propeller
737 781 InterPro IPR006691 DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat
32 507 InterPro IPR002205 DNA topoisomerase, type IIA, domain A
1 885 Hamap MF_01897 DNA gyrase subunit A [gyrA].
1 885 InterPro IPR005743 DNA gyrase, subunit A
32 522 Gene3D G3DSA:3.90.199.10 Topoisomerase II, domain 5
32 522 InterPro IPR013758 DNA topoisomerase, type IIA, domain A, alpha-beta
532 885 Gene3D G3DSA:2.120.10.90 -
532 885 InterPro IPR035516 DNA gyrase/topoisomerase IV, subunit A, C-terminal
236 334 FunFam G3DSA:3.30.1360.40:FF:000002 DNA gyrase subunit A
8 638 NCBIfam TIGR01063 DNA gyrase subunit A
371 493 Gene3D G3DSA:1.10.268.10 Topoisomerase, domain 3
371 493 InterPro IPR013757 DNA topoisomerase, type IIA, alpha-helical domain superfamily

3D Structure

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

3D visualization script Full viewer

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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 PA3168
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
5 0.287
6 0.25
2 0.21

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.

86 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…
ANP P0AES4 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
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
LFX Q8DPM2 361.4 Da LogP 1.54 TPSA 75.0 ✓ Ro5 ✓ Clean C[C@H]1COc2c3c(cc(c2N4CCN(CC4)C)F)C(=O)C(=CN31)…
MFX Q8DPM2 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…
SM8 P0AES5 932.3 Da LogP 3.00 TPSA 309.4 3 viol. ✓ Clean C[C@@H]1[C@H]([C@@H](C[C@@H](O1)c2ccc3c(c2O)[C@…
TR6 Q8DPM2 416.4 Da LogP 1.89 TPSA 101.5 ✓ Ro5 ✓ Clean c1cc(c(cc1F)F)N2C=C(C(=O)c3c2nc(c(c3)F)N4C[C@@H…
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.