Protein profile

PA4269

DNA-directed RNA polymerase subunit beta'

Genome: NC_002516.2

Gene: PA4269 rpoC Structure source: AlphaFold UniProt Q9HWC9
Amino acids 1399
Annotations 8
Features 42
PDB binders 29
Druggability 0.551

Overview

Basic information about this protein and its source genome.

Accession
PA4269
Gene
PA4269 rpoC
Status
annotated
Amino acids
1399
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
44.681
Human E-value
7.68e-20
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 0.551
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0000428 A protein complex that possesses DNA-directed RNA polymerase activity.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0003899 Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0008270 Binding to a zinc ion (Zn).
  • GO:0006351 The synthesis of an RNA transcript from a DNA template.

Sequence Features

Domain/signature hits from InterPro and related databases.

42 records
Show feature table
Start End DB Term Name
8 142 Gene3D G3DSA:4.10.860.120 RNA polymerase II, clamp domain
8 142 InterPro IPR044893 RNA polymerase Rpb1, clamp domain superfamily
489 643 Pfam PF04983 RNA polymerase Rpb1, domain 3
489 643 InterPro IPR007066 RNA polymerase Rpb1, domain 3
1023 1126 Gene3D G3DSA:2.40.50.100 -
15 813 CDD cd01609 RNAP_beta'_N
638 790 FunFam G3DSA:1.10.132.30:FF:000003 DNA-directed RNA polymerase subunit beta
1316 1376 FunFam G3DSA:1.10.150.390:FF:000002 DNA-directed RNA polymerase subunit beta''
907 1363 CDD cd02655 RNAP_beta'_C
1151 1215 Gene3D G3DSA:2.40.50.100 -
191 211 Coils Coil Coil
389 485 Pfam PF00623 RNA polymerase Rpb1, domain 2
389 485 InterPro IPR000722 RNA polymerase, alpha subunit
344 381 Pfam PF00623 RNA polymerase Rpb1, domain 2
344 381 InterPro IPR000722 RNA polymerase, alpha subunit
14 1387 Hamap MF_01322 DNA-directed RNA polymerase subunit beta' [rpoC].
14 1387 InterPro IPR012754 DNA-directed RNA polymerase, subunit beta-prime, bacterial type
370 413 Gene3D G3DSA:1.10.40.90 -
23 1363 PANTHER PTHR19376 DNA-DIRECTED RNA POLYMERASE
23 1363 InterPro IPR045867 DNA-directed RNA polymerase, subunit beta-prime
1368 1399 MobiDBLite mobidb-lite consensus disorder prediction
332 486 Gene3D G3DSA:2.40.40.20 -
766 1316 Pfam PF04998 RNA polymerase Rpb1, domain 5
766 1316 InterPro IPR007081 RNA polymerase Rpb1, domain 5
1135 1314 Gene3D G3DSA:1.10.1790.20 -
948 1022 Gene3D G3DSA:2.40.50.100 -
16 342 Pfam PF04997 RNA polymerase Rpb1, domain 1
16 342 InterPro IPR007080 RNA polymerase Rpb1, domain 1
638 790 Gene3D G3DSA:1.10.132.30 -
638 790 InterPro IPR038120 RNA polymerase Rpb1, funnel domain superfamily
235 514 SMART SM00663 rpolaneu7
235 514 InterPro IPR006592 RNA polymerase, N-terminal
12 132 FunFam G3DSA:4.10.860.120:FF:000001 DNA-directed RNA polymerase subunit beta
674 763 Pfam PF05000 RNA polymerase Rpb1, domain 4
674 763 InterPro IPR007083 RNA polymerase Rpb1, domain 4
489 637 Gene3D G3DSA:1.10.274.100 RNA polymerase Rpb1, domain 3
489 637 InterPro IPR042102 RNA polymerase Rpb1, domain 3 superfamily
19 1366 NCBIfam TIGR02386 DNA-directed RNA polymerase subunit beta'
19 1366 InterPro IPR012754 DNA-directed RNA polymerase, subunit beta-prime, bacterial type
1316 1376 Gene3D G3DSA:1.10.150.390 -
16 1363 SUPERFAMILY SSF64484 beta and beta-prime subunits of DNA dependent RNA-polymerase
372 413 FunFam G3DSA:1.10.40.90:FF:000001 DNA-directed RNA polymerase subunit beta

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 PA4269
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
2 0.551
3 0.208

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
0O2 P0A8T7 683.1 Da LogP -2.10 TPSA 392.2 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…
118 P0A8T7 430.2 Da LogP 3.06 TPSA 0.0 ✓ Ro5 ✓ Clean c1ccc(cc1)[Sb+](c2ccccc2)(c3ccccc3)c4ccccc4
1N7 P0A8T7 631.9 Da LogP 2.20 TPSA 164.4 2 viol. ✓ Clean C[C@H](CCC(=O)NCCC[N+](C)(C)CC(CS(=O)(=O)O)O)[C…
2TM Q8RQE8 481.2 Da LogP -2.10 TPSA 261.2 2 viol. ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
42S A7ZUK2 280.2 Da LogP 3.95 TPSA 44.6 ✓ Ro5 ✓ Clean c1ccc(cc1)N/C(=N\O)/c2cccc(c2)C(F)(F)F
42T A7ZUK2 483.3 Da LogP 6.71 TPSA 85.8 1 viol. ✓ Clean c1ccc(cc1)/N=C(\c2cc(cc(c2)NC(=O)Nc3c(cccc3Cl)C…
42U A7ZUK2 433.5 Da LogP 4.22 TPSA 56.0 ✓ Ro5 ✓ Clean c1cc(ccc1c2c(c[nH]n2)c3ccc(c(c3)C(F)(F)F)NCCN4C…
4C2 A7ZUK2 512.5 Da LogP 2.47 TPSA 121.6 1 viol. ✓ Clean Cc1c(c(on1)C)S(=O)(=O)NC2=C(C(=O)C2=O)N3CCC(CC3…
4C4 A7ZUK2 431.5 Da LogP 5.36 TPSA 105.8 1 viol. ✓ Clean CCCC/C(=C/C=C(\C)/C(=O)C1=C(C=C(OC1=O)[C@H](C)C…
4C6 A7ZUK2 443.5 Da LogP 2.46 TPSA 109.6 ✓ Ro5 ✓ Clean Cc1ccc(cc1)CC2CCN(CC2)C3=C(C(=O)C3=O)NS(=O)(=O)…
4OD P0A8T7 377.1 Da LogP 4.66 TPSA 44.6 ✓ Ro5 ✓ Clean c1cc(cc(c1)Br)/N=C(\c2ccc(c(c2)C(F)(F)F)F)/NO
4OE P0A8T7 324.3 Da LogP 5.04 TPSA 28.7 1 viol. ✓ Clean c1cc(ccc1c2c(cn[nH]2)c3ccc(c(c3)C(F)(F)F)F)F
88D P9WGY7 411.4 Da LogP 3.03 TPSA 58.2 ✓ Ro5 ✓ Clean Cc1ccccc1NC(=O)[C@@H](Cc2ccccc2)NC(=O)c3ccc[se]3
88G P9WGY7 358.4 Da LogP 3.97 TPSA 58.2 ✓ Ro5 ✓ Clean Cc1ccccc1NC(=O)[C@@H](Cc2ccccc2)NC(=O)c3ccccc3
APC Q8RQE8 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
C Q8RQE8 323.2 Da LogP -2.45 TPSA 177.4 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
C0L P9WGY7 527.7 Da LogP 6.04 TPSA 122.2 2 viol. ✓ Clean C/C=C/C/C=C(\C)/[C@@H](CC/C(=C/C=C(\C)/C(=C1C(=…
CH1 Q8RQE8 467.2 Da LogP -1.18 TPSA 250.2 2 viol. ✓ Clean C1[C@H](O[C@H]([C@@H]1O)N2C=CC(=NC2=O)N)CO[P@](…
DCP Q8RQE8 467.2 Da LogP -1.18 TPSA 250.2 2 viol. ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=…
DPO Q8RQE8 173.9 Da LogP -3.34 TPSA 135.6 ✓ Ro5 ✓ Clean [O-]P(=O)([O-])OP(=O)([O-])[O-]
FI8 P9WGY7 1058.1 Da LogP 6.23 TPSA 266.7 4 viol. ✓ Clean CCc1c(c(c(c(c1Cl)O)Cl)O)C(=O)O[C@@H]2[C@H](O[C@…
G4P Q8RQE8 603.2 Da LogP -2.22 TPSA 345.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
NE6 Q8RQE8 417.5 Da LogP 4.52 TPSA 99.1 ✓ Ro5 ✓ Clean CCC/C(=C/C=C(\C)/C(=O)C1C(=O)C=C(OC1=O)[C@H](C)…
POP Q8RQE8 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
PUM Q8RQE8 486.4 Da LogP -5.32 TPSA 290.0 1 viol. ✓ Clean [H]/N=C(/N)\NCC(=O)N([C@@H](CCC(=O)N)C(=O)NC[C@…
QZY P0A8T7 472.6 Da LogP 6.96 TPSA 78.9 1 viol. ✓ Clean CCN(Cc1ccccc1)C(=O)Nc2cc(sc2C(=O)O)c3ccc(cc3)Oc…
RFP P9WGY7 823.0 Da LogP 4.34 TPSA 220.1 3 viol. Alert Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…
STD Q8RQE8 600.7 Da LogP 2.46 TPSA 147.2 1 viol. ✓ Clean C[C@H]1[C@H]2C=C[C@@]3(CO3)[C@](O2)(O[C@@H]1[C@…
TGT Q8RQE8 416.3 Da LogP -3.13 TPSA 228.9 1 viol. ✓ Clean CC(=O)O[C@@H]1[C@@H]([C@H]([C@]2(CS[C@]([C@@H]1…

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.