Protein profile

PA4270

DNA-directed RNA polymerase subunit beta

Genome: NC_002516.2

Gene: rpoB PA4270 Structure source: AlphaFold UniProt Q51561
Amino acids 1357
Annotations 6
Features 43
PDB binders 35
Druggability 0.443

Overview

Basic information about this protein and its source genome.

Accession
PA4270
Gene
rpoB PA4270
Status
annotated
Amino acids
1357
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
42.424
Human E-value
2.17e-08
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 0.443
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • 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:0032549 Binding to a ribonucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked to ribose.
  • GO:0006351 The synthesis of an RNA transcript from a DNA template.

Sequence Features

Domain/signature hits from InterPro and related databases.

43 records
Show feature table
Start End DB Term Name
596 661 InterPro IPR019462 DNA-directed RNA polymerase, beta subunit, external 1 domain
600 1353 PANTHER PTHR20856 DNA-DIRECTED RNA POLYMERASE I SUBUNIT 2
600 1353 InterPro IPR015712 DNA-directed RNA polymerase, subunit 2
1281 1356 Pfam PF04560 RNA polymerase Rpb2, domain 7
1281 1356 InterPro IPR007641 RNA polymerase Rpb2, domain 7
447 718 Gene3D G3DSA:3.90.1100.10 -
838 943 FunFam G3DSA:2.40.50.150:FF:000001 DNA-directed RNA polymerase subunit beta
11 1357 SUPERFAMILY SSF64484 beta and beta-prime subunits of DNA dependent RNA-polymerase
949 1054 Gene3D G3DSA:6.10.140.1670 -
822 948 Gene3D G3DSA:2.40.50.150 -
822 948 InterPro IPR014724 RNA polymerase Rpb2, OB-fold
13 1357 Hamap MF_01321 DNA-directed RNA polymerase subunit beta [rpoB].
13 1357 InterPro IPR010243 DNA-directed RNA polymerase beta subunit, bacterial-type
26 504 Pfam PF04563 RNA polymerase beta subunit
26 504 InterPro IPR007644 RNA polymerase, beta subunit, protrusion
596 661 Pfam PF10385 RNA polymerase beta subunit external 1 domain
156 227 Pfam PF04561 RNA polymerase Rpb2, domain 2
156 227 InterPro IPR007642 RNA polymerase Rpb2, domain 2
359 459 Pfam PF04561 RNA polymerase Rpb2, domain 2
359 459 InterPro IPR007642 RNA polymerase Rpb2, domain 2
302 446 Gene3D G3DSA:3.90.1110.10 RNA polymerase Rpb2, domain 2
302 446 InterPro IPR037034 RNA polymerase Rpb2, domain 2 superfamily
1055 1257 Gene3D G3DSA:2.40.270.10 -
1055 1257 InterPro IPR037033 DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily
1080 1092 ProSitePatterns PS01166 RNA polymerases beta chain signature.
1080 1092 InterPro IPR007121 RNA polymerase, beta subunit, conserved site
157 272 FunFam G3DSA:3.90.1110.10:FF:000001 DNA-directed RNA polymerase subunit beta
343 451 FunFam G3DSA:3.90.1110.10:FF:000004 DNA-directed RNA polymerase subunit beta
18 178 Gene3D G3DSA:3.90.1100.10 -
595 661 Gene3D G3DSA:2.30.150.10 -
595 661 InterPro IPR042107 DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily
722 1279 Pfam PF00562 RNA polymerase Rpb2, domain 6
722 1279 InterPro IPR007120 DNA-directed RNA polymerase, subunit 2, hybrid-binding domain
27 1355 CDD cd00653 RNA_pol_B_RPB2
27 1355 InterPro IPR015712 DNA-directed RNA polymerase, subunit 2
719 800 Gene3D G3DSA:2.40.50.100 -
518 585 Pfam PF04565 RNA polymerase Rpb2, domain 3
518 585 InterPro IPR007645 RNA polymerase Rpb2, domain 3
1267 1320 Gene3D G3DSA:3.90.1800.10 RNA polymerase alpha subunit dimerisation domain
1267 1320 FunFam G3DSA:3.90.1800.10:FF:000001 DNA-directed RNA polymerase subunit beta
721 802 FunFam G3DSA:2.40.50.100:FF:000006 DNA-directed RNA polymerase subunit beta
8 1354 NCBIfam TIGR02013 DNA-directed RNA polymerase subunit beta
8 1354 InterPro IPR010243 DNA-directed RNA polymerase beta subunit, bacterial-type

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 PA4270
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
15 0.337
26 0.28
6 0.232
14 0.207

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.

93 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
118 P0A8V2 430.2 Da LogP 3.06 TPSA 0.0 ✓ Ro5 ✓ Clean c1ccc(cc1)[Sb+](c2ccccc2)(c3ccccc3)c4ccccc4
1N7 P0A8V2 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…
1RL P0A8V2 900.0 Da LogP 6.67 TPSA 216.4 3 viol. ✓ Clean CCN(CC)CCOc1cccc2c1N=C3c4c5c(c(c6c4C(=O)[C@](O6…
1RM P0A8V2 1035.2 Da LogP 6.62 TPSA 237.5 3 viol. ✓ Clean Cc1c(c2c3c4c1O[C@@](C4=O)(O/C=C/[C@@H]([C@H]([C…
2TM Q8RQE9 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 A7ZUK1 280.2 Da LogP 3.95 TPSA 44.6 ✓ Ro5 ✓ Clean c1ccc(cc1)N/C(=N\O)/c2cccc(c2)C(F)(F)F
42T A7ZUK1 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 A7ZUK1 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 A7ZUK1 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 A7ZUK1 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 A7ZUK1 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 P0A8V2 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 P0A8V2 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 P9WGY9 411.4 Da LogP 3.03 TPSA 58.2 ✓ Ro5 ✓ Clean Cc1ccccc1NC(=O)[C@@H](Cc2ccccc2)NC(=O)c3ccc[se]3
88G P9WGY9 358.4 Da LogP 3.97 TPSA 58.2 ✓ Ro5 ✓ Clean Cc1ccccc1NC(=O)[C@@H](Cc2ccccc2)NC(=O)c3ccccc3
APC Q8RQE9 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 Q8RQE9 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 P9WGY9 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 Q8RQE9 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 Q8RQE9 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 Q8RQE9 173.9 Da LogP -3.34 TPSA 135.6 ✓ Ro5 ✓ Clean [O-]P(=O)([O-])OP(=O)([O-])[O-]
FI8 P9WGY9 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 Q8RQE9 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…
KNG Q8RQE9 986.1 Da LogP 5.64 TPSA 292.6 4 viol. Alert Cc1c(c2c3c(cc(c2O)NC(=O)/C(=C\CC[C@@H]([C@@H]([…
NE6 Q8RQE9 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 Q8RQE9 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
PUM Q8RQE9 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 P0A8V2 472.6 Da LogP 6.96 TPSA 78.9 1 viol. ✓ Clean CCN(Cc1ccccc1)C(=O)Nc2cc(sc2C(=O)O)c3ccc(cc3)Oc…
RBT Q8RQE9 847.0 Da LogP 4.62 TPSA 205.5 2 viol. Alert Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…
RFP P9WGY9 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…
RFV Q8RQE9 699.8 Da LogP 4.60 TPSA 204.5 3 viol. ✓ Clean Cc1c(c2c3c(cc(c2O)NC(=O)C(=C/C=C/[C@@H]([C@@H](…
RPT Q8RQE9 877.0 Da LogP 5.65 TPSA 220.1 4 viol. Alert Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…
SRN P9WGY9 807.0 Da LogP 6.80 TPSA 161.2 2 viol. ✓ Clean C[C@H]1[C@H]2C\C=C\[C@H]3[C@@H]([C@H]4C[C@@H](O…
STD Q8RQE9 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 Q8RQE9 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.