KpKP13 Protein target profile

ribokinase-like superfamily protein

Accession: KP13_00525

Gene: AHE46741.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GI11
Length 508
Pocket druggability (P2Rank · AlphaFold DB model) 0.878
Direct ligand evidence 0 60 total records
Functional annotation 0 EC 7 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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 (%)
29.386 Lower values reduce human off-target concern.
Human E-value
1.74e-12
Gut microbiome similarity
2.0% 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
94.67 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) 0.878
Structure A0A0H3GI11
Pocket Pocket 1
Druggability (FPocket) 0.338
Structure A0A0H3GI11
Pocket Pocket 26
ColabFold model
P2Rank 0.905 · Pocket 1
FPocket 0.368 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 95 / 4744 genomes with a hit
Prevalence 2.0%

Sequence

Primary amino-acid sequence viewer.

MMDHTMTKNPDSIPYNIWPAEALRLAEREAADSLGLTLFELMQRAGEAAFQLASCAYPASAHWLILCGHGNNGGDGYVVARLAQAAGRRVTLLAVESDSPLPEEAQAAREAWLNAGGVIHAATIPWPDDISLIIDGLLGTGLRSAPRDPVAALIHQANHHPAPVVALDIPSGLNAQTGATPGAVVQADHTLTFIALKPGLLTGKARDVVGQLHHHALGLERWLAGQSTPLTRFCAAHLADWLPPRRATSHKGDHGKLVIVGGDRGTAGAIRMCGEAALRSGAGLVRVLTHPENVAPIVTVRPELMVDELTPQTLKAALEWADVVAIGPGLGQREWGRSALRTVESFNKPMVWDADALNLLAFNPDKRHNRVLTPHPGEAARLLNVSVAEIESDRLLSAQRLVKRYGGVVVLKGAGTVVASESGAMGIIDAGNAGMASGGMGDVLTGIIAALLGQHLTPYDAACAGCVAHGDAADRLAAREGTRGMLATDLFSTLRRVVNPDVIDVDHD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Subcellular localization

Localization
Unknown

Gene Ontology (GO)

7
  • GO:0052855 Catalysis of the reaction: (6S)-6beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine dinucleotide + ADP = AMP + H+ + NAD(P)H + phosphate.
  • GO:0016836 Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0046872 Binding to a metal ion.
  • GO:0052856 Catalysis of the reactions: (6R)-NADHX = (6S)-NADHX and (6R)-NADPHX = (6S)-NADPHX.
  • GO:0110051 A cellular process that, through single- or multi-step enzymatic reactions, repairs useless or toxic endogenous compounds, formed as by-products of primary metabolism, by converting them into useful metabolites.
  • GO:0046496 The chemical reactions and pathways involving nicotinamide nucleotides, any nucleotide that contains combined nicotinamide.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

33 records
Show feature table
Start End DB Term Name
15 504 PIRSF PIRSF017184 Nnr
15 504 InterPro IPR030677 Bifunctional NAD(P)H-hydrate repair enzyme Nnr
438 448 ProSitePatterns PS01050 YjeF C-terminal domain signature 2.
438 448 InterPro IPR017953 Carbohydrate kinase, predicted, conserved site
19 220 Hamap MF_01966 NAD(P)H-hydrate epimerase [nnrE].
19 220 InterPro IPR004443 YjeF N-terminal domain
234 501 ProSiteProfiles PS51383 YjeF C-terminal domain profile.
234 501 InterPro IPR000631 ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase
17 255 SUPERFAMILY SSF64153 YjeF N-terminal domain-like
17 255 InterPro IPR036652 YjeF N-terminal domain superfamily
230 500 FunFam G3DSA:3.40.1190.20:FF:000017 Multifunctional fusion protein
40 199 Pfam PF03853 YjeF-related protein N-terminus
40 199 InterPro IPR004443 YjeF N-terminal domain
24 220 NCBIfam TIGR00197 NAD(P)H-hydrate epimerase
24 220 InterPro IPR004443 YjeF N-terminal domain
232 499 NCBIfam TIGR00196 NAD(P)H-hydrate dehydratase
232 499 InterPro IPR000631 ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase
234 499 Hamap MF_01965 ADP-dependent (S)-NAD(P)H-hydrate dehydratase [nnrD].
234 499 InterPro IPR000631 ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase
23 225 ProSiteProfiles PS51385 YjeF N-terminal domain profile.
23 225 InterPro IPR004443 YjeF N-terminal domain
233 498 SUPERFAMILY SSF53613 Ribokinase-like
233 498 InterPro IPR029056 Ribokinase-like
16 224 Gene3D G3DSA:3.40.50.10260 -
16 224 InterPro IPR036652 YjeF N-terminal domain superfamily
15 225 FunFam G3DSA:3.40.50.10260:FF:000003 Multifunctional fusion protein
247 490 CDD cd01171 YXKO-related
247 490 InterPro IPR000631 ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase
230 500 Gene3D G3DSA:3.40.1190.20 -
230 500 InterPro IPR029056 Ribokinase-like
236 499 PANTHER PTHR12592 ATP-DEPENDENT (S)-NAD(P)H-HYDRATE DEHYDRATASE FAMILY MEMBER
258 495 Pfam PF01256 Carbohydrate kinase
258 495 InterPro IPR000631 ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase

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
0.878
Likely same site as FPocket 26 5.2 Å 17 shared residues 77% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.841
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.352
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.098
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.018
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #26
0.338
Likely same site as P2Rank 1 5.2 Å 17 shared residues 77% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:130-130
UniProt: Binding site:134-140
UniProt: Binding site:163-163
UniProt: Binding site:166-166
UniProt: Binding site:264-264
UniProt: Binding site:324-324
UniProt: Binding site:370-370
UniProt: Binding site:407-411
UniProt: Binding site:436-436
UniProt: Binding site:437-437
UniProt: Binding site:66-70
UniProt: Binding site:67-67
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_A0A0H3GI11
AlphaFold DB full sequence Viewing
ColabFold KP13_00525
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.

60 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 10 records from similar proteins
Structural ligands 10 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
A3P PDB via homolog 427.2 Da · LogP -1.75 · TPSA 232.6 Open detail RCSB PDB
ADQ PDB via homolog Detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
AP5 PDB via homolog Detail RCSB PDB
APR 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
A3P RCSB PDB Q9X024 427.2 Da LogP -1.75 TPSA 232.6 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ADQ RCSB PDB Q9X024 589.3 Da LogP -3.92 TPSA 311.7 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP RCSB PDB J9VIT7 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)…
AP5 RCSB PDB P94368 916.4 Da LogP -2.33 TPSA 480.5 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
APR RCSB PDB P94368 559.3 Da LogP -3.28 TPSA 291.5 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
B4P RCSB PDB P94368 836.4 Da LogP -2.45 TPSA 434.0 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
B6P RCSB PDB P94368 996.3 Da LogP -2.21 TPSA 527.0 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BA3 RCSB PDB P94368 756.4 Da LogP -2.56 TPSA 387.4 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
NAX RCSB PDB P94368 683.5 Da LogP -3.49 TPSA 337.8 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
NPW RCSB PDB P94368 763.4 Da LogP -3.37 TPSA 384.4 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.