Protein profile

KP13_32224

DNA polymerase IV

Genome: KpKP13

Gene: dinB AHE46193.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GN39
Amino acids 370
Annotations 9
Features 32
PDB binders 32
Druggability 0.791

Overview

Basic information about this protein and its source genome.

Accession
KP13_32224
Gene
dinB AHE46193.1
Status
annotated
Amino acids
370
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
55.814
Human E-value
1.34e-10
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
92.65

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 0.791
Structure A0A0H3GN39
Pocket Pocket 2
P2Rank 0.557
Structure A0A0H3GN39
Pocket Pocket 1
ColabFold model
FPocket 0.776 · Pocket 1
P2Rank 0.581 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 153 / 4744 genomes with a hit
Normalized 0.032

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0003887 Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time.
  • GO:0003684 Binding to damaged DNA.
  • GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • 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:0042276 The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions and causes an increase in the endogenous mutation level. For example, in E. coli, a low fidelity DNA polymerase, pol V, copies lesions that block replication fork progress. This produces mutations specifically targeted to DNA template damage sites, but it can also produce mutations at undamaged sites.
  • GO:0009432 An error-prone process for repairing damaged microbial DNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
40 92 FunFam G3DSA:3.40.1170.60:FF:000001 DNA polymerase IV
23 204 ProSiteProfiles PS50173 UmuC domain profile.
23 204 InterPro IPR001126 UmuC domain
26 173 Pfam PF00817 impB/mucB/samB family
26 173 InterPro IPR001126 UmuC domain
11 17 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
259 366 Pfam PF11799 impB/mucB/samB family C-terminal domain
259 366 InterPro IPR017961 DNA polymerase, Y-family, little finger domain
1 2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
3 10 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
18 370 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
40 92 Gene3D G3DSA:3.40.1170.60 -
20 360 PANTHER PTHR11076 DNA REPAIR POLYMERASE UMUC / TRANSFERASE FAMILY MEMBER
87 184 FunFam G3DSA:3.30.70.270:FF:000002 DNA polymerase IV
188 216 Pfam PF11798 IMS family HHH motif
188 216 InterPro IPR024728 DNA polymerase type-Y, HhH motif
20 368 Hamap MF_01113 DNA polymerase IV [dinB].
20 368 InterPro IPR022880 DNA polymerase IV
260 370 Gene3D G3DSA:3.30.1490.100 -
260 370 InterPro IPR036775 DNA polymerase, Y-family, little finger domain superfamily
24 358 CDD cd03586 PolY_Pol_IV_kappa
24 358 InterPro IPR022880 DNA polymerase IV
260 370 FunFam G3DSA:3.30.1490.100:FF:000002 DNA polymerase IV
23 184 Gene3D G3DSA:3.30.70.270 -
23 184 InterPro IPR043128 Reverse transcriptase/Diguanylate cyclase domain
1 17 Phobius SIGNAL_PEPTIDE Signal peptide region
186 247 FunFam G3DSA:1.10.150.20:FF:000019 DNA polymerase IV
260 368 SUPERFAMILY SSF100879 Lesion bypass DNA polymerase (Y-family), little finger domain
260 368 InterPro IPR036775 DNA polymerase, Y-family, little finger domain superfamily
19 253 SUPERFAMILY SSF56672 DNA/RNA polymerases
19 253 InterPro IPR043502 DNA/RNA polymerase superfamily
185 246 Gene3D G3DSA:1.10.150.20 -

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_A0A0H3GN39
AlphaFold full sequence Viewing
ColabFold KP13_32224
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
2 0.791

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 7.04 0.364
2 2.8 0.086

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.

85 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
0G4 Q97W02 486.2 Da LogP -0.53 TPSA 232.8 2 viol. ✓ Clean C1[C@H](O[C@H](S1)COP(=O)(O)OP(=O)(NP(=O)(O)O)O…
0G8 Q97W02 389.2 Da LogP -0.36 TPSA 183.4 ✓ Ro5 ✓ Clean C1[C@H](O[C@H](S1)COP(=O)(O)OP(=O)(O)O)N2C=CC(=…
0KX Q47155 466.2 Da LogP -1.61 TPSA 253.0 2 viol. ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(N…
0OH Q9UNA4 501.2 Da LogP 0.06 TPSA 249.7 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@]4([C@@H]3C4…
0OJ Q9UNA4 501.2 Da LogP -0.15 TPSA 249.7 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@]34C[C@H]3[C@@H]([C@H](C4)…
1FZ Q47155 481.2 Da LogP -1.59 TPSA 246.9 1 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O…
2LF Q97W02 345.2 Da LogP -1.49 TPSA 185.8 ✓ Ro5 ✓ Clean C1[C@@H]([C@H]2[C@H](c3nc4c(n3[C@@H]1O2)N=C(NC4…
2TM Q47155 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…
3TT Q97W02 468.2 Da LogP -0.67 TPSA 232.8 2 viol. ✓ Clean C1[C@H](O[C@H](S1)COP(=O)(O)OP(=O)(NP(=O)(O)O)O…
8GT Q47155 539.2 Da LogP -3.04 TPSA 319.1 3 viol. ✓ Clean C([C@@H]1[C@H]([C@H]([C@@H](O1)N2C3=C(C(=O)NC(=…
A38 Q97W02 347.2 Da LogP -1.54 TPSA 185.8 ✓ Ro5 ✓ Clean c1nc(c2c(n1)N(C(=O)N2)[C@H]3C[C@@H]([C@H](O3)CO…
ADI Q9UNA4 395.2 Da LogP 0.31 TPSA 192.1 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3CC[C@H](O3)CO[P@@](=O)(…
AF Q97W02 181.2 Da LogP 2.84 TPSA 26.0 ✓ Ro5 ✓ Clean c1ccc-2c(c1)Cc3c2ccc(c3)N
BAP Q97W02 304.3 Da LogP 2.90 TPSA 60.7 ✓ Ro5 ✓ Clean c1cc2ccc3cc4c(c5c3c2c(c1)cc5)C[C@H]([C@H]([C@@H…
DCP Q9UBZ9 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@@](=…
DCT Q97W02 451.2 Da LogP -0.15 TPSA 230.0 1 viol. ✓ Clean C1C[C@@H](O[C@@H]1CO[P@](=O)(O)O[P@](=O)(O)OP(=…
DDS Q97W02 475.2 Da LogP 0.43 TPSA 238.7 1 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3CC[C@H](O3)CO[P@@](=O)(…
DDY Q97W02 371.2 Da LogP -0.27 TPSA 183.4 ✓ Ro5 ✓ Clean C1C[C@@H](O[C@@H]1CO[P@@](=O)(O)OP(=O)(O)O)N2C=…
DG3 Q97W02 491.2 Da LogP -0.28 TPSA 258.6 2 viol. ✓ Clean c1nc2c(n1[C@H]3CC[C@H](O3)CO[P@@](=O)(O)O[P@](=…
DGT Q97W02 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…
DOC Q97W02 291.2 Da LogP -0.39 TPSA 136.9 ✓ Ro5 ✓ Clean C1C[C@@H](O[C@@H]1COP(=O)(O)O)N2C=CC(=NC2=O)N
DPO Q47155 173.9 Da LogP -3.34 TPSA 135.6 ✓ Ro5 ✓ Clean [O-]P(=O)([O-])OP(=O)([O-])[O-]
DT Q97W02 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…
DTP Q97W02 491.2 Da LogP -0.60 TPSA 258.9 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@]…
DZ4 Q97W02 490.2 Da LogP -1.03 TPSA 261.7 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@@…
FTD Q97W02 409.2 Da LogP -0.25 TPSA 180.9 ✓ Ro5 ✓ Clean C1[C@H](O[C@H](S1)COP(=O)(O)OP(=O)(O)O)N2CC(=C(…
LTP Q97W02 387.2 Da LogP -1.30 TPSA 203.7 ✓ Ro5 ✓ Clean C1[C@H]([C@@H](O[C@@H]1N2C=CC(=NC2=O)N)COP(=O)(…
POP Q97W02 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
TTP Q97W02 482.2 Da LogP -1.16 TPSA 244.1 2 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…
TTW Q47155 481.2 Da LogP -1.59 TPSA 246.9 1 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O…
XG4 Q97W02 506.2 Da LogP -1.73 TPSA 281.7 3 viol. ✓ Clean c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(N[P…
YYY Q97W02 387.2 Da LogP -1.30 TPSA 203.7 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=…

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.