KpKP13 Protein target profile

Helicase superfamily protein

Accession: KP13_01338

Gene: AHE46598.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A6A8EMP7
Length 1180
Pocket druggability (P2Rank · AlphaFold DB model) 0.94
Direct ligand evidence 0 57 total records
Functional annotation 0 EC 4 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
Hit
Human identity (%)
36.111 Lower values reduce human off-target concern.
Human E-value
7.57e-08
Gut microbiome similarity
0.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
85.53 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.94
Structure A0A6A8EMP7
Pocket Pocket 1
Druggability (FPocket) 0.883
Structure A0A6A8EMP7
Pocket Pocket 22
ColabFold model
P2Rank 0.986 · Pocket 1
FPocket 0.312 · Pocket 82
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 11 / 4744 genomes with a hit
Prevalence 0.2%

Sequence

Primary amino-acid sequence viewer.

MLKLEEIKKDAQVRGIVEGQVVRVVTVEQIGEHALTVYYKDSKGVLAERMLFRSDEMALELATVGRAWAFDADGGDFKLGLEAYRISQAALFDPMMAVNMANVDPLPHQISAVYEYMLPKQPLRYVLADDPGAGKTIMAGLFISELLLRADARRIMVVSPGSLTEQWQDELFEKFGLQFEIFSKEKQEQCATGNFFTETDRLICRLDQLSRSEELQEKLRNTDWDLIIVDEAHKLSANYFGNKINKTKRFALGELLGSICRHFLLMTATPHNGKEEDFQVWMSLLDSDRFYGKFREGAHKVDITDMMRRMVKEELLTFDGTPLFPERRAYTANYDLSSLEASLYEQVTTYVREEMNRADKLDNKKKNTVGFALTQLQRRLASSPEAIYQSLKRRRNRLKDKLAEMKLLARGQKAKLTGVAETLGSYTVTKQLDLPDNWDELDEDLSAEEYELYAEQVADQATAAETILELDAEILSLKDLEQQALLLVQSGNDKKWEQLSALLQDSPEMKNRDGSRRKLIIFTEHKDTLNYLRQRVGDLLGQSNAVRVIYGGTNRDERRKIQSEFRSDPTVLVLIATDAAGEGVNLQNANLMVNYDLPWNPNRLEQRFGRIHRIGQKEVCHLWNIVANETREGEVFQKLFAKLEIEKQALGGKVFDILGEAFDNVSLKQLLMDAIRYGEDPAVRARMDQAIEGALDSDHLKEIMRRNALVESHMGMEGLYAIKEQMEKAEARRLQPFFIRAFFQEAFQMLGGDLREREQGRYEIRHVPAVIRERDRTIGESRTPVLPRYERVCFEKQLTRPTGKVLAELLHPVHPLMHSVLDLTLQAHRGKLKQGAVLVDPADDCDEPRLIIMLEHSVRETAEQAKSIASRRLQFVAIDKACQASYAGWAPHLDLVPISEGDLTLVQDILCSPWLSQPLEPLALQLASEKLVPEHFAEVKTRRELQADKTLAAVHERLIKEINYWQDRYLKLSDDVKSGKQPRMQPENARRRVDELTARLQQRTTELTALKQVVSSTPVVIGSALVIPQGLLAKRKGEVMFSPDAASRAHIERVAMQAVTDAEQALGHMVIDVAADKCGWDITARPPLKSDGSLPQDRHIEVKGRSKGQITITVSRNEILYALNQADKFLLAIVLVEGDKAEGPYYIRQPFTKEPDLGVASINYDLADLLARSTNAEGSL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

4
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0140658 An activity, driven by ATP hydrolysis, that modulates the contacts between histones and DNA, resulting in a change in chromosome architecture within the nucleosomal array, leading to chromatin remodeling.
  • GO:0004386 Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
993 1013 Coils Coil Coil
526 615 SMART SM00490 helicmild6
526 615 InterPro IPR001650 Helicase, C-terminal
124 369 Pfam PF00176 SNF2-related domain
124 369 InterPro IPR000330 SNF2, N-terminal
498 666 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile.
498 666 InterPro IPR001650 Helicase, C-terminal
116 288 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile.
116 288 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
95 291 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
95 291 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
105 309 CDD cd18011 DEXDc_RapA
433 645 Gene3D G3DSA:3.40.50.300 -
433 645 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
222 657 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
222 657 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
107 686 PANTHER PTHR10799 SNF2/RAD54 HELICASE FAMILY
101 304 SMART SM00487 ultradead3
101 304 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
493 626 CDD cd18793 SF2_C_SNF
1051 1143 Pfam PF13020 Protein NO VEIN, C-terminal
1051 1143 InterPro IPR024975 Protein NO VEIN, C-terminal
495 615 Pfam PF00271 Helicase conserved C-terminal domain
495 615 InterPro IPR001650 Helicase, C-terminal
1180 1180 Coils Coil Coil
388 415 Coils Coil Coil
102 423 Gene3D G3DSA:3.40.50.10810 -
102 423 InterPro IPR038718 SNF2-like, N-terminal domain superfamily

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

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.94
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.825
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.729
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.451
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.386
Likely same site as FPocket 22 3.1 Å 10 shared residues 77% of smaller site
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #22
0.883
Likely same site as P2Rank 5 3.1 Å 10 shared residues 77% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #2
0.75 Unusual size
Show in viewer
Surrounding area
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_A0A6A8EMP7
AlphaFold DB full sequence Viewing
ColabFold KP13_01338
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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AGS PDB via homolog 523.2 Da · LogP -1.51 · TPSA 262.1 Open detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
BEF PDB via homolog Detail RCSB PDB
DC PDB via homolog Detail RCSB PDB
DG PDB via homolog Detail RCSB PDB

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
AGS RCSB PDB P32657 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP RCSB PDB Q14839 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)…
BEF RCSB PDB P22082 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
DC RCSB PDB P32657 307.2 Da LogP -1.42 TPSA 157.1 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O…
DG RCSB PDB P32657 347.2 Da LogP -1.54 TPSA 185.8 ✓ Ro5 ✓ Clean c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N…
DT RCSB PDB P32657 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…
KH2 RCSB PDB G2QDW1 221.3 Da LogP 0.55 TPSA 57.2 ✓ Ro5 ✓ Clean C[N+]1(CCCCC1)CCCS(=O)(=O)[O-]

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.

Cross-references

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