KpKP13 Protein target profile

NAD-dependent deacetylase

Accession: KP13_31489

Gene: AHE45251.1 npdA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A060VNR5
Length 276
Pocket druggability (P2Rank · AlphaFold DB model) 0.924
Direct ligand evidence 0 156 total records
Functional annotation 1 EC 6 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 (%)
45.161 Lower values reduce human off-target concern.
Human E-value
7.65e-31
Gut microbiome similarity
2.9% 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
87.94 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) 0.924
Structure A0A060VNR5
Pocket Pocket 1
Druggability (FPocket) 0.501
Structure A0A060VNR5
Pocket Pocket 2
ColabFold model
P2Rank 0.925 · Pocket 1
FPocket 0.516 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 136 / 4744 genomes with a hit
Prevalence 2.9%

Sequence

Primary amino-acid sequence viewer.

MQSRRLHRLSRFRRNKRRLRDRLRQRIFFREDRMKPEAMAKPRVVVLTGAGISAESGIKTFRAADGLWEEHRVEDVATPEGFARDPALVQAFYNARRRQLQSPEIKPNAAHLALARLEDLLGDHFLLVTQNIDNLHERAGNRRVIHMHGELLKVRCSWSGQVLEWTGDVTAEDKCHCCQFPAALRPHVVWFGEMPLGMDEIYSALADADIFIAIGTSGHVYPAAGFVHEARLHGAHTVELNLEPSQVGSEFAEKHYGLASEVVPAFIDKLLQENAL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0036055 Catalysis of the reaction: N(6)-succinyl-L-lysyl-[protein] + NAD+ + H2O = 2''-O-succinyl-ADP-D-ribose + nicotinamide + L-lysyl-[protein].
  • GO:0036054 Catalysis of the reaction: N(6)-malonyl-L-lysyl-[protein] + NAD+ + H2O = 2''-O-malonyl-ADP-D-ribose + nicotinamide + L-lysyl-[protein].
  • GO:0070403 Binding to the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0017136 Catalysis of the reaction: N(6)-acetyl-L-lysyl-[histone] + NAD+ + H2O = L-lysyl-[protein] + 2''-O-acetyl-ADP-D-ribose + nicotinamide. This reaction transfers an acetyl group from a histone to NAD, producing nicotinamide.
  • GO:0008270 Binding to a zinc ion (Zn).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
57 276 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
42 271 SUPERFAMILY SSF52467 DHS-like NAD/FAD-binding domain
42 271 InterPro IPR029035 DHS-like NAD/FAD-binding domain superfamily
44 52 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
58 194 Gene3D G3DSA:3.30.1600.10 SIR2/SIRT2 'Small Domain'
58 194 InterPro IPR026591 Sirtuin, catalytic core small domain superfamily
40 270 PANTHER PTHR47651 NAD-DEPENDENT HISTONE DEACETYLASE HST4
1 43 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
53 56 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
42 272 Hamap MF_01121 NAD-dependent protein deacylase [cobB].
42 272 InterPro IPR027546 Sirtuin, class III
49 222 Pfam PF02146 Sir2 family
49 222 InterPro IPR003000 Sirtuin family
1 56 Phobius SIGNAL_PEPTIDE Signal peptide region
22 273 ProSiteProfiles PS50305 Sirtuin catalytic domain profile.
22 273 InterPro IPR026590 Sirtuin family, catalytic core domain
44 264 Gene3D G3DSA:3.40.50.1220 -
42 267 CDD cd01412 SIRT5_Af1_CobB
42 267 InterPro IPR027546 Sirtuin, class III

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.

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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
0.924
Likely same site as FPocket 2 1.0 Å 36 shared residues 92% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.034
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.01
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.006
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #2
0.501 Unusual size
Likely same site as P2Rank 1 1.0 Å 36 shared residues 92% of smaller site
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_A0A060VNR5
AlphaFold DB full sequence Viewing
ColabFold KP13_31489
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.

156 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 106 records from similar proteins
Structural ligands 21 0 loaded crystals
Measured bioactivity 85 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
0L1 PDB via homolog 146.1 Da · LogP 0.72 · TPSA 74.6 Open detail RCSB PDB
3NP PDB via homolog Detail RCSB PDB
APR PDB via homolog Detail RCSB PDB
BJW PDB via homolog Detail RCSB PDB
BV8 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
0L1 RCSB PDB Q6DHI5 146.1 Da LogP 0.72 TPSA 74.6 ✓ Ro5 ✓ Clean C(CCC(=O)O)CC(=O)O
3NP RCSB PDB Q6DHI5 119.1 Da LogP -0.26 TPSA 80.4 ✓ Ro5 ✓ Clean C(C[N+](=O)[O-])C(=O)O
APR RCSB PDB O28597 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)…
BJW RCSB PDB Q6DHI5 1179.1 Da LogP 2.19 TPSA 421.9 3 viol. ✓ Clean CC(C)NC(=O)[C@H](Cc1c[nH]c2c1cccc2)NC(=O)[C@H](…
BV8 RCSB PDB Q6DHI5 1180.1 Da LogP 1.08 TPSA 445.3 3 viol. ✓ Clean CC(C)NC(=O)[C@H](Cc1c[nH]c2c1cccc2)NC(=O)[C@H](…
BVT RCSB PDB Q6DHI5 1180.1 Da LogP 0.96 TPSA 434.0 3 viol. ✓ Clean CC(C)NC(=O)[C@H](Cc1c[nH]c2c1cccc2)NC(=O)[C@H](…
CNA RCSB PDB Q9NXA8 662.5 Da LogP -2.35 TPSA 309.0 3 viol. ✓ Clean c1cc(c[n+](c1)[C@@H]2C[C@@H]([C@H]([C@H]2O)O)CO…
DZK RCSB PDB Q6DHI5 240.3 Da LogP 1.85 TPSA 74.6 ✓ Ro5 ✓ Clean c1ccc(cc1)CS[C@@H](CC(=O)O)C(=O)O
E9N RCSB PDB Q6DHI5 240.3 Da LogP 1.85 TPSA 74.6 ✓ Ro5 ✓ Clean c1ccc(cc1)CS[C@H](CC(=O)O)C(=O)O
F9V RCSB PDB Q6DHI5 194.2 Da LogP 1.33 TPSA 74.6 ✓ Ro5 ✓ Clean c1ccc(cc1)C(CC(=O)O)C(=O)O
GUA RCSB PDB Q6DHI5 132.1 Da LogP 0.33 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)CC(=O)O
GZB RCSB PDB Q6DHI5 179.2 Da LogP 0.50 TPSA 66.4 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)NCC(=O)O
HLY RCSB PDB Q6DHI5 290.3 Da LogP -0.70 TPSA 149.9 ✓ Ro5 ✓ Clean C[C@@](CC(=O)NCCCC[C@@H](C(=O)O)N)(CC(=O)O)O
JO3 RCSB PDB Q6DHI5 132.1 Da LogP 0.18 TPSA 74.6 ✓ Ro5 ✓ Clean CC(CC(=O)O)C(=O)O
KMQ RCSB PDB P75960-2 613.4 Da LogP -1.68 TPSA 280.5 3 viol. ✓ Clean C/C=C/CO[C@@H]1[C@@H]([C@H](O[C@@H]1O)COP(=O)(O…
NCA RCSB PDB O30124 122.1 Da LogP 0.18 TPSA 56.0 ✓ Ro5 ✓ Clean c1cc(cnc1)C(=O)N
NX6 RCSB PDB Q6DHI5 267.2 Da LogP 0.84 TPSA 112.9 ✓ Ro5 ✓ Clean c1ccc(cc1)COC(=O)N[C@@H](CC(=O)O)C(=O)O
OAD RCSB PDB O28597 601.4 Da LogP -2.71 TPSA 297.6 3 viol. ✓ Clean CC(=O)O[C@@H]1[C@@H]([C@H](O[C@@H]1O)CO[P@@](=O…
SU8 RCSB PDB Q6DHI5 174.2 Da LogP 1.35 TPSA 74.6 ✓ Ro5 ✓ Clean CCCC[C@H](CC(=O)O)C(=O)O
SUH RCSB PDB Q6DHI5 132.1 Da LogP 0.18 TPSA 74.6 ✓ Ro5 ✓ Clean C[C@@H](CC(=O)O)C(=O)O
WOC RCSB PDB Q6DHI5 146.1 Da LogP 0.57 TPSA 74.6 ✓ Ro5 ✓ Clean CC(C)(CC(=O)O)C(=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.

Chemistry

ChEMBL CHEMBL4091790 ChEMBL CHEMBL4064460 ChEMBL CHEMBL5199270 ChEMBL CHEMBL4065067 ChEMBL CHEMBL4068735 ChEMBL CHEMBL4073655 ChEMBL CHEMBL4092751 ChEMBL CHEMBL4100475 ChEMBL CHEMBL4636862 ChEMBL CHEMBL4091258 ChEMBL CHEMBL5209031 ChEMBL CHEMBL5172115 ChEMBL CHEMBL4100351 ChEMBL CHEMBL5188575 ChEMBL CHEMBL4065953 ChEMBL CHEMBL4083471 ChEMBL CHEMBL4085990 ChEMBL CHEMBL4084850 ChEMBL CHEMBL4101463 ChEMBL CHEMBL4079616 ChEMBL CHEMBL46469 ChEMBL CHEMBL4078223 ChEMBL CHEMBL5177283 ChEMBL CHEMBL4097208 ChEMBL CHEMBL4079212 ChEMBL CHEMBL4092610 ChEMBL CHEMBL4063400 ChEMBL CHEMBL5398650 ChEMBL CHEMBL4068365 ChEMBL CHEMBL5197912 ChEMBL CHEMBL5185695 ChEMBL CHEMBL4093875 ChEMBL CHEMBL5416344 ChEMBL CHEMBL4073959 ChEMBL CHEMBL4086401 ChEMBL CHEMBL5182606 ChEMBL CHEMBL4080031 ChEMBL CHEMBL4104295 ChEMBL CHEMBL5201717 ChEMBL CHEMBL5192844 ChEMBL CHEMBL4100041 ChEMBL CHEMBL4286528 ChEMBL CHEMBL5182719 ChEMBL CHEMBL5209009 ChEMBL CHEMBL5195052 ChEMBL CHEMBL5402569 ChEMBL CHEMBL5408550 ChEMBL CHEMBL4094165 ChEMBL CHEMBL4083597 ChEMBL CHEMBL4074580 ChEMBL CHEMBL5398355 ChEMBL CHEMBL4092289 ChEMBL CHEMBL5192524 ChEMBL CHEMBL4105234 ChEMBL CHEMBL4071831 ChEMBL CHEMBL4096566 ChEMBL CHEMBL4067303 ChEMBL CHEMBL4094852 ChEMBL CHEMBL4073591 ChEMBL CHEMBL4105624 ChEMBL CHEMBL4082324 ChEMBL CHEMBL4104916 ChEMBL CHEMBL5424757 ChEMBL CHEMBL4068050 ChEMBL CHEMBL4290465 ChEMBL CHEMBL5171330 ChEMBL CHEMBL5197726 ChEMBL CHEMBL1201346 ChEMBL CHEMBL2165275 ChEMBL CHEMBL224864 ChEMBL CHEMBL4287164 ChEMBL CHEMBL4287527 ChEMBL CHEMBL4295059 ChEMBL CHEMBL4758325 ChEMBL CHEMBL4780319 ChEMBL CHEMBL4785262 ChEMBL CHEMBL4860183 ChEMBL CHEMBL4869330 ChEMBL CHEMBL4875043 ChEMBL CHEMBL5171546 ChEMBL CHEMBL5204662 ChEMBL CHEMBL5205516 ChEMBL CHEMBL5420622 ChEMBL CHEMBL5424599 ChEMBL SVR