Protein profile

KP13_01361

DNA-directed RNA polymerase subunit beta'

Genome: KpKP13

Gene: AHE46938.1 rpoC Structure source: AlphaFold + ColabFold UniProt A0A0H3GGP0
Amino acids 1407
Annotations 8
Features 46
PDB binders 35
Druggability 0.373

Overview

Basic information about this protein and its source genome.

Accession
KP13_01361
Gene
AHE46938.1 rpoC
Status
annotated
Amino acids
1407
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
44.681
Human E-value
9.73e-20
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
98.081
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
86.11

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 0.373
Structure A0A0H3GGP0
Pocket Pocket 100
P2Rank 0.704
Structure A0A0H3GGP0
Pocket Pocket 1
ColabFold model
FPocket 0.723 · Pocket 116
P2Rank 0.782 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 354 / 4744 genomes with a hit
Normalized 0.075

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: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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0006351 The synthesis of an RNA transcript from a DNA template.
  • 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:0000287 Binding to a magnesium (Mg) ion.
  • GO:0008270 Binding to a zinc ion (Zn).

Sequence Features

Domain/signature hits from InterPro and related databases.

46 records
Show feature table
Start End DB Term Name
184 218 Coils Coil Coil
948 1022 FunFam G3DSA:2.40.50.100:FF:000019 DNA-directed RNA polymerase subunit beta
19 1367 NCBIfam TIGR02386 DNA-directed RNA polymerase subunit beta'
19 1367 InterPro IPR012754 DNA-directed RNA polymerase, subunit beta-prime, bacterial type
1275 1295 Coils Coil Coil
373 416 Gene3D G3DSA:1.10.40.90 -
15 813 CDD cd01609 RNAP_beta'_N
907 1363 CDD cd02655 RNAP_beta'_C
1151 1215 Gene3D G3DSA:2.40.50.100 -
948 1022 Gene3D G3DSA:2.40.50.100 -
7 128 Gene3D G3DSA:4.10.860.120 RNA polymerase II, clamp domain
7 128 InterPro IPR044893 RNA polymerase Rpb1, clamp domain superfamily
10 1374 Hamap MF_01322 DNA-directed RNA polymerase subunit beta' [rpoC].
10 1374 InterPro IPR012754 DNA-directed RNA polymerase, subunit beta-prime, bacterial type
1023 1126 FunFam G3DSA:2.40.50.100:FF:000016 DNA-directed RNA polymerase subunit beta
332 486 Gene3D G3DSA:2.40.40.20 -
235 514 SMART SM00663 rpolaneu7
235 514 InterPro IPR006592 RNA polymerase, N-terminal
1316 1377 FunFam G3DSA:1.10.150.390:FF:000002 DNA-directed RNA polymerase subunit beta''
1316 1375 Gene3D G3DSA:1.10.150.390 -
1135 1314 Gene3D G3DSA:1.10.1790.20 -
16 1363 SUPERFAMILY SSF64484 beta and beta-prime subunits of DNA dependent RNA-polymerase
15 342 Pfam PF04997 RNA polymerase Rpb1, domain 1
15 342 InterPro IPR007080 RNA polymerase Rpb1, domain 1
489 644 Pfam PF04983 RNA polymerase Rpb1, domain 3
489 644 InterPro IPR007066 RNA polymerase Rpb1, domain 3
1151 1215 FunFam G3DSA:2.40.50.100:FF:000012 DNA-directed RNA polymerase subunit beta
25 1363 PANTHER PTHR19376 DNA-DIRECTED RNA POLYMERASE
25 1363 InterPro IPR045867 DNA-directed RNA polymerase, subunit beta-prime
638 790 Gene3D G3DSA:1.10.132.30 -
638 790 InterPro IPR038120 RNA polymerase Rpb1, funnel domain superfamily
1023 1126 Gene3D G3DSA:2.40.50.100 -
674 763 Pfam PF05000 RNA polymerase Rpb1, domain 4
674 763 InterPro IPR007083 RNA polymerase Rpb1, domain 4
638 790 FunFam G3DSA:1.10.132.30:FF:000003 DNA-directed RNA polymerase subunit beta
489 637 Gene3D G3DSA:1.10.274.100 RNA polymerase Rpb1, domain 3
489 637 InterPro IPR042102 RNA polymerase Rpb1, domain 3 superfamily
489 637 FunFam G3DSA:1.10.274.100:FF:000002 DNA-directed RNA polymerase subunit beta
372 413 FunFam G3DSA:1.10.40.90:FF:000001 DNA-directed RNA polymerase subunit beta
12 132 FunFam G3DSA:4.10.860.120:FF:000001 DNA-directed RNA polymerase subunit beta
392 485 Pfam PF00623 RNA polymerase Rpb1, domain 2
392 485 InterPro IPR000722 RNA polymerase, alpha subunit
344 393 Pfam PF00623 RNA polymerase Rpb1, domain 2
344 393 InterPro IPR000722 RNA polymerase, alpha subunit
766 1315 Pfam PF04998 RNA polymerase Rpb1, domain 5
766 1315 InterPro IPR007081 RNA polymerase Rpb1, domain 5

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 + 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_A0A0H3GGP0
AlphaFold full sequence Viewing
ColabFold KP13_01361
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
100 0.373
7 0.333
12 0.237

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 Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 14.1 0.711
2 8.41 0.448
3 5.89 0.288
4 5.28 0.248
5 3.8 0.147

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.

87 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…
2KH P04050 483.2 Da LogP -2.93 TPSA 267.2 2 viol. ✓ Clean C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)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
AHW P04050 186.3 Da LogP 3.41 TPSA 9.2 ✓ Ro5 ✓ Clean CCc1ccc2ccc(cc2c1)OC
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@@](=…
DGT P04050 507.2 Da LogP -1.31 TPSA 278.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(O)O…
DPO P0A8T7 173.9 Da LogP -3.34 TPSA 135.6 ✓ Ro5 ✓ Clean [O-]P(=O)([O-])OP(=O)([O-])[O-]
DUT P04050 468.1 Da LogP -1.47 TPSA 244.1 2 viol. ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@@](=…
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@…
G2P P04050 521.2 Da LogP -2.22 TPSA 289.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
G4P P0A8T7 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-]
PPV P04050 178.0 Da LogP -0.81 TPSA 124.3 ✓ Ro5 ✓ Clean OP(=O)(O)OP(=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.