Protein target profile

KP13_01714

DNA helicase II

Genome: KpKP13 Gene: uvrD AHE46982.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GGJ9
Length 720
Pocket druggability 0.038
Direct ligand evidence 0 52 total records
Functional annotation 1 EC 13 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
3.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
95.972 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
87.83 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.038
Structure A0A0H3GGJ9
Pocket Pocket 33
P2Rank 0.649
Structure A0A0H3GGJ9
Pocket Pocket 1
ColabFold model
FPocket 0.446 · Pocket 29
P2Rank 0.683 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 165 / 4744 genomes with a hit
Prevalence 3.5%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

Primary amino-acid sequence viewer.

MDVSYLLDSLNDKQREAVAASRTNMLVLAGAGSGKTRVLVHRIAWLLSVENCSPYSIMAVTFTNKAAAEMRHRIGQLMGTTQGGMWVGTFHGLAHRLLRAHHLDANLPQDFQILDSEDQLRLLKRLIKAMNLDEKQWPPRQAMWYINSQKDEGLRPHHIQSYGNPVEQTWQKVYQAYQEACDRAGLVDFAELLLRAHELWLNKPHILQHYRERFTNILVDEFQDTNNIQYAWIRLLAGDTGKVMIVGDDDQSIYGWRGAQVENIQRFLNDFPGAETIRLEQNYRSTSNILSAANALIENNNGRLGKKLWTDGADGEPISLYCAFNDLDEARFVVNRIKTWQENGGALEQCAILYRSNAQSRVLEEALLQASMPYRIYGGMRFFERQEIKDALSYLRLIANRNDDAAFERVVNTPTRGIGDRTLDVVRQTSRDRQLTLWQASRELLKEKALAGRAASALQRFMELIDALAQETTDMPLHVQTDRVIKDSGLRAMYEQEKGEKGQTRIENLEELVTATRQFSYNEEDEDLMPLQAFLSHAALEAGEGQADTWQDAVQLMTLHSAKGLEFPQVFIVGVEEGMFPSQMALDEGGRLEEERRLAYVGVTRAMQKLTLTYAETRRLYGKEVYHRPSRFIGELPQECVEEVRLRATVSRPVNHQRLGAPIAESDTGYKLGQRVRHPKFGEGTIVNLEGSGEHSRLQVAFQGQGIKWLVAAYARLEAV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 13 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

13
  • GO:0006268 OBSOLETE. The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0003678 Unwinding of a DNA helix, driven by ATP hydrolysis.
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0033202 A protein complex that possesses DNA helicase activity.
  • GO:0043138 Unwinding a DNA helix in the direction 5' to 3', driven by ATP hydrolysis.
  • GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • GO:0042802 Binding to an identical protein or proteins.
  • GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
  • GO:0000725 A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous DNA region.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
281 636 Gene3D G3DSA:3.40.50.300 -
281 636 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
8 286 ProSiteProfiles PS51198 UvrD-like DNA helicase ATP-binding domain profile.
8 286 InterPro IPR014016 UvrD-like helicase, ATP-binding domain
114 187 FunFam G3DSA:1.10.10.160:FF:000002 DNA helicase
114 187 Gene3D G3DSA:1.10.10.160 -
114 187 InterPro IPR013986 DExx box DNA helicase domain superfamily
280 383 FunFam G3DSA:3.40.50.300:FF:001201 ATP-dependent DNA helicase UvrD2
287 564 ProSiteProfiles PS51217 UvrD-like DNA helicase C-terminal domain profile.
287 564 InterPro IPR014017 UvrD-like DNA helicase, C-terminal
10 271 Pfam PF00580 UvrD/REP helicase N-terminal domain
10 271 InterPro IPR014016 UvrD-like helicase, ATP-binding domain
7 642 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
7 642 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
6 718 NCBIfam TIGR01075 DNA helicase UvrD
6 718 InterPro IPR005753 DNA helicase, ATP-dependent, UvrD type
9 647 PANTHER PTHR11070 UVRD / RECB / PCRA DNA HELICASE FAMILY MEMBER
9 647 InterPro IPR000212 DNA helicase, UvrD/REP type
10 274 Gene3D G3DSA:3.40.50.300 -
10 274 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
285 614 CDD cd18807 SF1_C_UvrD
382 538 FunFam G3DSA:1.10.486.10:FF:000001 DNA helicase
382 538 Gene3D G3DSA:1.10.486.10 PCRA; domain 4
277 616 Pfam PF13361 UvrD-like helicase C-terminal domain
277 616 InterPro IPR014017 UvrD-like DNA helicase, C-terminal
11 283 CDD cd17932 DEXQc_UvrD

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.649
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.63
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.404
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.1
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.075
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:29-36
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GGJ9
AlphaFold DB full sequence Viewing
ColabFold KP13_01714
ColabFold full sequence Loaded

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.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ANP PDB via homolog 506.2 Da · LogP -2.06 · TPSA 281.9 Open detail RCSB PDB
MGF PDB via homolog Detail RCSB PDB
ZINC12360002 ZINC proposed compound · Tanimoto 0.810 Detail ZINC
ZINC12360703 ZINC proposed compound · Tanimoto 0.810 Detail ZINC
ZINC12503599 ZINC proposed compound · Tanimoto 0.810 Detail ZINC

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
ANP RCSB PDB P03018 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)…
MGF RCSB PDB P03018 81.3 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean F[Mg-](F)F

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.