Protein target profile

KP13_03495

Histone deacetylase superfamily protein

Genome: KpKP13 Gene: AHE45871.1 3D evidence: Experimental + ColabFold model UniProt A0A377Z5F6
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Length 371
Pocket druggability 0.974
Direct ligand evidence 0 151 total records
Functional annotation 1 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.

Main supporting evidence

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.97, P2Rank 0.75). Use the 3D pocket comparison to verify whether they identify the same site. Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. Strong predicted binding pocket FPocket selected-pocket score 0.97. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.75. Review the complete evidence below

Risks to review

Human similarity Top human hit identity: 36.207%. This target also has a predicted binding pocket (FPocket 0.97) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 16 of 4744 screened genomes (0.3%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.97) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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 (%)
36.207 Lower values reduce human off-target concern.
Human E-value
2.04e-35
Gut microbiome similarity
0.3% 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.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
98.26 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.974
Structure 9GN6
Pocket Pocket 1
P2Rank 0.75
Structure 9GN7
Pocket Pocket 1
ColabFold model
FPocket 0.213 · Pocket 2
P2Rank 0.191 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 16 / 4744 genomes with a hit
Prevalence 0.3%

Cross-references

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

Sequence

UniProt A0A377Z5F6

Structure

PDB 9GN6 PDB 9GLB PDB 9GN7 PDB 9GN1

Chemistry

ChEMBL N9W ChEMBL CHEMBL4636622 ChEMBL CHEMBL419758 ChEMBL CHEMBL3970950 ChEMBL CHEMBL4784006 ChEMBL CHEMBL236129 ChEMBL CHEMBL5189146 ChEMBL CHEMBL3693786 ChEMBL CHEMBL1934905 ChEMBL CHEMBL1934898 ChEMBL CHEMBL1934892 ChEMBL CHEMBL1934894 ChEMBL CHEMBL1934896 ChEMBL CHEMBL5192796 ChEMBL CHEMBL5195750 ChEMBL CHEMBL1934891 ChEMBL CHEMBL4452620 ChEMBL CHEMBL1934908 ChEMBL CHEMBL2047684 ChEMBL CHEMBL2047685 ChEMBL CHEMBL5172611 ChEMBL CHEMBL1934903 ChEMBL CHEMBL1934895 ChEMBL AH7 ChEMBL CHEMBL5175813 ChEMBL CHEMBL1934904 ChEMBL CHEMBL5193136 ChEMBL CHEMBL1934900 ChEMBL CHEMBL550625 ChEMBL CHEMBL561154 ChEMBL TSN ChEMBL CHEMBL1934909 ChEMBL CHEMBL1934906 ChEMBL CHEMBL2425955 ChEMBL CHEMBL4096623 ChEMBL CHEMBL4170768 ChEMBL CHEMBL4206537 ChEMBL CHEMBL4215954 ChEMBL CHEMBL4218266 ChEMBL CHEMBL4469488 ChEMBL CHEMBL4550214 ChEMBL CHEMBL4777296 ChEMBL CHEMBL478727 ChEMBL CHEMBL4846435 ChEMBL CHEMBL4867598 ChEMBL CHEMBL5076794 ChEMBL CHEMBL5089854 ChEMBL CHEMBL5185866 ChEMBL CHEMBL5198026 ChEMBL CHEMBL5423557 ChEMBL CHEMBL5437069 ChEMBL CHEMBL5438457 ChEMBL CHEMBL5572911 ChEMBL CLT ChEMBL N4R

Sequence

Primary amino-acid sequence viewer.

MKRKTGFFFDERCFWHSTGLHAVTLPVGGWVQPPAGGGHAESPETKRRMKNLMDVSGLTPQLALRSAAPASLEDLRRIHPDSYLERFKAISDNGGGMLGKEAPLGPGSYEIACLSAGLACAAVEAVLKGELDNAYSLSRPPGHHCLPDQSMGFCFLANIPIAVERAKAQLGLGKVAIIDWDVHHGNGTQHIYLQRDDVLTISLHQDGCFPPGYAGEDDRGVGAGEGYNINIPLLAGAGDDSWRYALETIVIPALARFEPELIIIACGYDANAMDPLARMQLHSDSFRAMTEQVQQAADRLCGGKLVMVHEGGYAESYVPFCGLAVMEALSGIRTEVQDPLLEFIQQQQPRAAFAQFQREAIDRLGQQFGLQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0004407 Removal of an acetyl group from a lysine residue in a histone.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0046872 Binding to a metal ion.
  • GO:0040029 A process that modulates the frequency, rate or extent of gene expression through chromatin remodeling either by modifying higher order chromatin fiber structure, nucleosomal histones, or cytosine methylation of DNA. Once established, this regulation may be maintained over many cell divisions. It can also be heritable in the absence of the instigating signal.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
5 364 CDD cd09996 HDAC_classII_1
39 327 Pfam PF00850 Histone deacetylase domain
39 327 InterPro IPR023801 Histone deacetylase domain
24 330 PANTHER PTHR48252 HISTONE DEACETYLASE 2-RELATED
1 350 SUPERFAMILY SSF52768 Arginase/deacetylase
1 350 InterPro IPR023696 Ureohydrolase domain superfamily
259 269 PRINTS PR01270 Histone deacetylase superfamily signature
259 269 InterPro IPR000286 Histone deacetylase family
140 163 PRINTS PR01270 Histone deacetylase superfamily signature
140 163 InterPro IPR000286 Histone deacetylase family
174 189 PRINTS PR01270 Histone deacetylase superfamily signature
174 189 InterPro IPR000286 Histone deacetylase family
2 371 Gene3D G3DSA:3.40.800.20 Histone deacetylase domain
2 371 InterPro IPR037138 Histone deacetylase 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.

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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 · FPocket

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

Site 1 FPocket #1
0.974
Unusual size
Show in viewer
Surrounding area
All structural evidence 4 experimental · 1 predicted

Structural evidence

4 + 1

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
PDB 9GN6
X-ray 1.95 Å A
100.0% 1-371
PDBe RCSB PDBj File
Viewing
PDB 9GLB
X-ray 2.10 Å C
100.0% 1-371
PDBe RCSB PDBj File
Loaded
PDB 9GN7
X-ray 2.18 Å A
100.0% 1-371
PDBe RCSB PDBj File
Loaded
PDB 9GN1
X-ray 2.35 Å A
100.0% 1-371
PDBe RCSB PDBj File
Loaded
ColabFold KP13_03495
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.

151 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 101 records from similar proteins
Structural ligands 46 0 loaded crystals
Measured bioactivity 55 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3YP PDB via homolog 157.2 Da · LogP 1.46 · TPSA 49.3 Open detail RCSB PDB
5OG PDB via homolog Detail RCSB PDB
5OJ PDB via homolog Detail RCSB PDB
5OK PDB via homolog Detail RCSB PDB
6DK 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
3YP RCSB PDB
1ZZ3
Q70I53 157.2 Da LogP 1.46 TPSA 49.3 ✓ Ro5 ✓ Clean C1CCC(C1)CCC(=O)NO
5OG RCSB PDB
5EEN
F8W4B7 318.4 Da LogP 2.01 TPSA 95.5 ✓ Ro5 ✓ Clean c1ccc(cc1)NS(=O)(=O)c2cccc(c2)/C=C/C(=O)NO
5OJ RCSB PDB
5EF7
F8W4B7 314.3 Da LogP 1.37 TPSA 89.9 ✓ Ro5 ✓ Clean c1ccc(cc1)N(CCO)C(=O)Cc2ccc(cc2)C(=O)NO
5OK RCSB PDB
5EFB
F8W4B7 342.4 Da LogP 1.90 TPSA 95.5 ✓ Ro5 ✓ Clean c1ccc(cc1)S(=O)(=O)Nc2cccc(c2)C#CC=CC(=O)NO
6DK RCSB PDB
5G10
Q9HXM1 319.3 Da LogP 3.21 TPSA 69.6 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)CCCCCCC(C(F)(F)F)(O)O
7H1 RCSB PDB
5G11
Q9HXM1 480.2 Da LogP 3.94 TPSA 78.4 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)C(C(C(C(C(C(C(=O)NO)(F)F)(F)F)(…
9RB RCSB PDB
5LI3
Q9HXM1 299.3 Da LogP 2.97 TPSA 91.9 ✓ Ro5 Alert Cc1c(c(n(n1)C)C)/N=N/c2ccc(cc2)/C=C/C(=O)NO
A6I RCSB PDB
6PZU
F8W4B7 484.6 Da LogP 2.27 TPSA 145.9 ✓ Ro5 ✓ Clean C[C@@H](C(=O)NCc1ccc(cc1)C(=O)NO)NC(=O)[C@H](CC…
AGJ RCSB PDB
5WGK
F8W4B7 328.4 Da LogP 1.37 TPSA 89.9 ✓ Ro5 ✓ Clean c1ccc(cc1)CC(=O)N(CCO)Cc2ccc(cc2)C(=O)NO
AH4 RCSB PDB
5WGL
F8W4B7 433.5 Da LogP 4.13 TPSA 107.5 ✓ Ro5 ✓ Clean c1ccc(cc1)N(c2ccccc2)c3ncc(cn3)C(=O)NCCCCCCC(=O…
BHO RCSB PDB
6CSR
F8W4B7 137.1 Da LogP 0.81 TPSA 49.3 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)NO
BTB RCSB PDB
6DVM
F8W4B7 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
C65 RCSB PDB
5G3W
Q70I53 267.3 Da LogP 3.62 TPSA 74.0 ✓ Ro5 Alert c1ccc(cc1)/N=N/c2ccc(cc2)/C=C/C(=O)NO
CF3 RCSB PDB
2GH6
Q70I53 301.3 Da LogP 4.10 TPSA 46.2 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)CCCCCCC(=O)C(F)(F)F
E1Z RCSB PDB
5G0H
F8W4B7 302.4 Da LogP 2.58 TPSA 69.6 ✓ Ro5 ✓ Clean C[C@@H](/C=C(\C)/C=C/C(=O)NO)C(=O)c1ccc(cc1)N(C…
F0Z RCSB PDB
6GJK
Q70I53 192.3 Da LogP 1.72 TPSA 24.4 ✓ Ro5 ✓ Clean c1ccc(c(c1)C2=NCCCN2)S
F1Y RCSB PDB
6CGP
A7YT55 310.4 Da LogP 3.15 TPSA 78.7 ✓ Ro5 ✓ Clean CCCc1c(n2ccccc2n1)Nc3ccc(cc3)C(=O)NO
F9P RCSB PDB
6CSQ
F8W4B7 143.2 Da LogP 1.07 TPSA 49.3 ✓ Ro5 ✓ Clean C1CCC(CC1)C(=O)NO
FBJ RCSB PDB
6CSS
F8W4B7 127.1 Da LogP 0.60 TPSA 49.3 ✓ Ro5 ✓ Clean C1CC=C(C1)C(=O)NO
FBM RCSB PDB
6CSP
F8W4B7 141.2 Da LogP 0.99 TPSA 49.3 ✓ Ro5 ✓ Clean C1CCC(=CC1)C(=O)NO
FGY RCSB PDB
6CW8
F8W4B7 525.6 Da LogP 1.28 TPSA 165.7 2 viol. ✓ Clean C[C@@H](C(=O)NCc1ccccc1)NC(=O)[C@H](CC(=O)NCC(C…
FKS RCSB PDB
5EFH
F8W4B7 258.3 Da LogP 0.73 TPSA 78.5 ✓ Ro5 ✓ Clean C(CCC(C(F)(F)F)(O)O)CCNCCCN
FLC RCSB PDB
5WGL
F8W4B7 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
HB7 RCSB PDB
6DVN
F8W4B7 460.5 Da LogP 2.83 TPSA 102.0 ✓ Ro5 ✓ Clean CN(C)c1ccc(cc1)C(=O)N(Cc2ccc(cc2)C(=O)NO)CC(=O)…
HBG RCSB PDB
6DVL
F8W4B7 437.5 Da LogP 3.51 TPSA 98.7 ✓ Ro5 ✓ Clean Cc1cc(cc(c1)C(=O)N(Cc2ccc(cc2)C(=O)NO)CC(=O)NC3…
HBJ RCSB PDB
6DVM
F8W4B7 460.5 Da LogP 3.46 TPSA 102.0 ✓ Ro5 ✓ Clean Cc1ccc(cc1)NC(=O)CN(Cc2ccc(cc2)C(=O)NO)C(=O)c3c…
HBV RCSB PDB
6DVO
F8W4B7 346.4 Da LogP 3.59 TPSA 52.6 ✓ Ro5 ✓ Clean CN(Cc1ccc(cc1F)C(=O)NO)CC23CC4CC(C2)CC(C4)C3
K70 RCSB PDB
5W5K
F8W4B7 350.4 Da LogP 2.31 TPSA 65.2 ✓ Ro5 ✓ Clean c1cc2c(nc1)[N+](=C3C=CC=CC3=S2)Cc4ccc(cc4)C(=O)…
LBH RCSB PDB
5EF8
F8W4B7 349.4 Da LogP 3.33 TPSA 77.2 ✓ Ro5 Alert Cc1c(c2ccccc2[nH]1)CCNCc3ccc(cc3)/C=C/C(=O)NO
MCM RCSB PDB
5EFK
F8W4B7 175.2 Da LogP 1.68 TPSA 56.2 ✓ Ro5 ✓ Clean CC1=CC(=O)Oc2c1ccc(c2)N
MLT RCSB PDB
6GJK
Q70I53 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
NH4 RCSB PDB
5EEF
F8W4B7 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
P5Y RCSB PDB
6PYE
F8W4B7 510.5 Da LogP 3.70 TPSA 113.2 1 viol. ✓ Clean c1ccc(cc1)Cn2c(nnn2)CN(Cc3ccc(cc3)C(=O)NO)C(=O)…
P6Y RCSB PDB
6PZO
F8W4B7 339.3 Da LogP 2.15 TPSA 91.3 ✓ Ro5 ✓ Clean c1cc(c(nc1)C(F)(F)F)C(=O)NCc2ccc(cc2)C(=O)NO
P7D RCSB PDB
6PZR
F8W4B7 349.4 Da LogP 1.31 TPSA 91.6 ✓ Ro5 ✓ Clean CN(C)Cc1ccc(cc1)S(=O)(=O)n2ccc(c2)/C=C/C(=O)NO
P7J RCSB PDB
6PZS
F8W4B7 302.4 Da LogP 2.97 TPSA 61.4 ✓ Ro5 ✓ Clean CC1([C@@H]2CC[C@H]([C@H]1C2)CNCc3ccc(cc3)C(=O)N…
P7V RCSB PDB
6Q0Z
F8W4B7 283.1 Da LogP 2.22 TPSA 75.4 ✓ Ro5 ✓ Clean c1cc(ccc1c2nc(co2)C(=O)NO)Br
QCM RCSB PDB
6UOC
F8W4B7 421.5 Da LogP 4.55 TPSA 90.9 ✓ Ro5 ✓ Clean CCN(CC)Cc1ccc2cc(ccc2c1)COC(=O)Nc3ccc(cc3)C(=O)…
QCP RCSB PDB
6UO3
F8W4B7 312.4 Da LogP 3.18 TPSA 78.4 ✓ Ro5 ✓ Clean CC(C)[C@@H](c1ccccc1)C(=O)Nc2ccc(cc2)C(=O)NO
QQD RCSB PDB
6V79
F8W4B7 373.5 Da LogP 4.24 TPSA 65.5 ✓ Ro5 ✓ Clean CC1(c2ccccc2N([C@@H]1c3cccnc3)Cc4ccc(cc4)C(=O)N…
QQG RCSB PDB
6V7A
F8W4B7 351.5 Da LogP 2.79 TPSA 55.8 ✓ Ro5 ✓ Clean CN1CC2(CCN(CC2)Cc3ccc(cc3)C(=O)NO)c4c1cccc4
R5G RCSB PDB
6VNR
F8W4B7 325.3 Da LogP 1.93 TPSA 103.6 ✓ Ro5 ✓ Clean c1cc(ccc1Cn2ccc3c2cc(cc3)C(=O)NO)C(=O)NO
SHH RCSB PDB
1ZZ1
Q70I53 264.3 Da LogP 2.47 TPSA 78.4 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)CCCCCCC(=O)NO
UFJ RCSB PDB
6WYQ
F8W4B7 390.2 Da LogP 3.08 TPSA 78.4 ✓ Ro5 ✓ Clean c1cc(ccc1NC(=O)CCCCCCC(=O)NO)I
UFS RCSB PDB
6WYP
F8W4B7 477.6 Da LogP 4.44 TPSA 124.6 ✓ Ro5 ✓ Clean C#CCCCC(=O)Nc1ccc(cc1)C(=O)c2ccc(cc2)NC(=O)CCCC…
W45 RCSB PDB
6MR5
F8W4B7 345.3 Da LogP 4.16 TPSA 34.0 ✓ Ro5 ✓ Clean c1cn(c2c1cc(c(c2)Cl)Cl)CCCCCNC(=O)CS

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.