Natural Product: NPC478319

Natural Product IDNPC478319
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 WMUMHAZHWIUBPN-UONOGXRCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 14756407
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0002449] Amines
          • [CHEMONTID:0002460] Alkanolamines
            • [CHEMONTID:0001897] 1,2-aminoalcohols

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey WMUMHAZHWIUBPN-UONOGXRCSA-N
Standard InCHI InChI=1S/C14H31NO/c1-3-4-5-6-7-8-9-10-11-12-14(16)13(2)15/h13-14,16H,3-12,15H2,1-2H3/t13-,14+/m0/s1
SMILES CCCCCCCCCCC[C@H]([C@H](C)N)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   229.24 Volume:   270.487
?
Van der Waals volume.
Dense:   0.848 LogP:   3.61
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.005
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.04
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   11.0 Rigid Bonds:   0.0
TPSA:   46.25
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   3.0 Rings:   0.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.532 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.745 Fsp3:   1.0
MCE-18:   2.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.476 Fluc inhibitor:   0.001
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.02
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.736 Promiscuous compounds:   0.313

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.03 MDCK Permeability:   -4.804
Pgp-inhibitor:   0.0 Pgp-substrate:   0.51
PAMPA:   0.056
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.453
20% Bioavailability (F20%):   0.84 30% Bioavailability (F30%):   0.935
50% Bioavailability (F50%):   0.949

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.025 MRP1:   0.892
Plasma Protein Binding (PPB):   99.376% Volume Distribution (VD):   1.259
Fu: 2.489%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.434
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.275
BSEP inhibitor:   0.034

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.024
CYP2C19-inhibitor:   0.928 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.07 CYP2C9-substrate:   0.851
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.7
HLM stability:   0.002
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  5.089 Half-life (T1/2):  0.768

ADMET: Toxicity

hERG Blockers:  0.324 hERG Blockers (10um):  0.717
Human Hepatotoxicity (H-HT):  0.515 Drug-induced Liver Injury (DILI):  0.059
AMES Toxicity:  0.189 Rat Oral Acute Toxicity:  0.227
Maximum Recommended Daily Dose:  0.281 Skin Sensitization:  0.947
Carcinogencity:  0.357 Eye Corrosion:  0.989
Eye Irritation:  0.985 Respiratory Toxicity:  0.862
Drug-induced Neurotoxicity:  0.182 Ototoxicity:  0.31
Hematotoxicity:  0.224 Drug-induced Nephrotoxicity:  0.16
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.039
A549 Cytotoxicity:  0.325 Hek293 Cytotoxicity:  0.11
BCF:   1.916
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   4.873
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.471
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.332
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO32702 xestospongia sp. Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[11908959]
NPO32702 xestospongia sp. Species Petrosiidae Eukaryota n.a. Caledonian n.a. PMID[1453184]
NPO32702 xestospongia sp. Species Petrosiidae Eukaryota n.a. Thai n.a. PMID[14640515]
NPO32702 xestospongia sp. Species Petrosiidae Eukaryota n.a. thai n.a. PMID[15217287]
NPO32702 xestospongia sp. Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[1710256]
NPO32702 xestospongia sp. Species Petrosiidae Eukaryota n.a. coral reef habitat at a depth of approximately 20 m from the sea bed surface, at Sangalaki, Indonesia (2 04 59 N, 118 23 41 E) 1996-MAR PMID[20503979]
NPO32702 xestospongia sp. Species Petrosiidae Eukaryota n.a. Indonesia n.a. PMID[20503979]
NPO32702 xestospongia sp. Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[31260310]
NPO32702 xestospongia sp. Species Petrosiidae Eukaryota n.a. Philippine n.a. PMID[7473578]
NPO32702 xestospongia sp. Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[7798966]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



  NP Quantity Composition/Concentration

Organism ID Organism Name Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



 Biological Activity

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. GI = 100.0 % PMID[21955681]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 4500.0 nM PMID[21955681]
NPT2 Others Unspecified n.a. Activity = 95.0 % PMID[1710256]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC478319 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC121062
1.0 High Similarity NPC29222
1.0 High Similarity NPC96966
1.0 High Similarity NPC602997
0.8947 High Similarity NPC474322
0.7083 Intermediate Similarity NPC123814
0.68 Remote Similarity NPC168308
0.68 Remote Similarity NPC302569
0.6538 Remote Similarity NPC604436
0.6296 Remote Similarity NPC478318
0.5714 Remote Similarity NPC319034
0.5714 Remote Similarity NPC1748
0.5714 Remote Similarity NPC72324
0.5714 Remote Similarity NPC97967
0.5714 Remote Similarity NPC193062
0.5556 Remote Similarity NPC8979
0.5333 Remote Similarity NPC47333
0.5312 Remote Similarity NPC113224
0.5312 Remote Similarity NPC489448
0.5312 Remote Similarity NPC601273
0.5238 Remote Similarity NPC110884
0.5217 Remote Similarity NPC66124
0.5152 Remote Similarity NPC319131

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC478319 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
1.0 High Similarity NPD3214 Discontinued
0.7083 Intermediate Similarity NPD3215 Phase 2

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data