Natural Product: NPC486386

Natural Product IDNPC486386
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
ZOMPRRFBBCCHKC-GJQUWGJHSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 ZOMPRRFBBCCHKC-GJQUWGJHSA-N
Standard InCHI InChI=1S/C51H84O24/c1-20(19-67-44-38(61)36(59)33(56)28(16-52)70-44)8-13-50(65)22(3)51(66)31(75-50)15-27-25-7-6-23-14-24(9-11-48(23,4)26(25)10-12-49(27,51)5)69-47-43(74-45-39(62)35(58)32(55)21(2)68-45)41(64)42(30(18-54)72-47)73-46-40(63)37(60)34(57)29(17-53)71-46/h6,20-22,24-47,52-66H,7-19H2,1-5H3/t20-,21+,22-,24+,25-,26+,27+,28-,29-,30-,31?,32+,33-,34+,35-,36+,37-,38-,39-,40-,41+,42-,43-,44-,45+,46+,47-,48+,49+,50-,51-/m1/s1
SMILES C[C@H](CC[C@@]1([C@@H](C)[C@]2(C(C[C@H]3[C@@H]4CC=C5C[C@H](CC[C@]5(C)[C@H]4CC[C@]23C)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O[C@H]2[C@@H]([C@@H]([C@H]([C@@H](CO)O2)O)O)O)O)O[C@H]2[C@@H]([C@@H]([C@H]([C@H](C)O2)O)O)O)O1)O)O)CO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1080.54 Volume:   1021.973
?
Van der Waals volume.
Dense:   1.057 LogP:   -0.19
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.669
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.212
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   48.0
TPSA:   386.52
?
Topological Polar Surface Area.
H-Bond Acceptor:   24.0
H-Bond Donor:   15.0 Rings:   9.0
Heavy Atoms:   24.0

MedChem Properties

QED Drug-Likeness Score:   0.07 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.906 Fsp3:   0.961
MCE-18:   183.58
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.577 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.002
?
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:   0.295 Promiscuous compounds:   0.098

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.059 MDCK Permeability:   -5.004
Pgp-inhibitor:   0.0 Pgp-substrate:   0.994
PAMPA:   1.0
?
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):   0.566
20% Bioavailability (F20%):   0.461 30% Bioavailability (F30%):   0.998
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.007
Plasma Protein Binding (PPB):   39.435% Volume Distribution (VD):   -0.37
Fu: 37.522%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.026
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.058 CYP3A4-substrate:   0.07
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.802
HLM stability:   0.031
?
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):  -0.441 Half-life (T1/2):  4.155

ADMET: Toxicity

hERG Blockers:  0.005 hERG Blockers (10um):  0.009
Human Hepatotoxicity (H-HT):  0.427 Drug-induced Liver Injury (DILI):  0.781
AMES Toxicity:  0.959 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.005 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.482 Drug-induced Nephrotoxicity:  0.927
Genotoxicity:  0.016 RPMI-8226 Immunitoxicity:  0.365
A549 Cytotoxicity:  0.965 Hek293 Cytotoxicity:  0.802
BCF:   1.12
?
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:   3.239
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.371
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.544
?
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
NPO16818 Trillium tschonoskii Species Melanthiaceae Eukaryota n.a. n.a. n.a. PMID[32870000]
NPO16818 Trillium tschonoskii Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16818 Trillium tschonoskii Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16818 Trillium tschonoskii Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16818 Trillium tschonoskii Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16818 Trillium tschonoskii Species Melanthiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

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
NPT2 Others Unspecified n.a. FC = 1.9 n.a. PMID[32870000]
NPT2 Others Unspecified n.a. FC = 8.8 n.a. PMID[32870000]

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 NPC486386 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
0.9789 High Similarity NPC254255
0.7524 Intermediate Similarity NPC73243
0.7524 Intermediate Similarity NPC244086
0.7524 Intermediate Similarity NPC84956
0.7383 Intermediate Similarity NPC247037
0.7182 Intermediate Similarity NPC249265
0.717 Intermediate Similarity NPC124677
0.7117 Intermediate Similarity NPC23808
0.7117 Intermediate Similarity NPC87998
0.6964 Remote Similarity NPC486384
0.6944 Remote Similarity NPC475182
0.6637 Remote Similarity NPC194207
0.6637 Remote Similarity NPC22779
0.6552 Remote Similarity NPC308140
0.6429 Remote Similarity NPC102016
0.6429 Remote Similarity NPC95051
0.6422 Remote Similarity NPC98696
0.6356 Remote Similarity NPC232054
0.6339 Remote Similarity NPC480555
0.6339 Remote Similarity NPC150372
0.6337 Remote Similarity NPC165439
0.6273 Remote Similarity NPC40440
0.6204 Remote Similarity NPC94272
0.6154 Remote Similarity NPC218571
0.6154 Remote Similarity NPC487615
0.6071 Remote Similarity NPC470433
0.6071 Remote Similarity NPC46190
0.6071 Remote Similarity NPC171073
0.5983 Remote Similarity NPC475333
0.5983 Remote Similarity NPC224098
0.5983 Remote Similarity NPC208383
0.5917 Remote Similarity NPC480553
0.5909 Remote Similarity NPC306991
0.5763 Remote Similarity NPC269297
0.5763 Remote Similarity NPC222202
0.575 Remote Similarity NPC480554
0.5739 Remote Similarity NPC248746
0.5739 Remote Similarity NPC122819
0.5714 Remote Similarity NPC13193
0.5702 Remote Similarity NPC486388
0.568 Remote Similarity NPC480556
0.5603 Remote Similarity NPC469348
0.5583 Remote Similarity NPC309278
0.5565 Remote Similarity NPC42482
0.5556 Remote Similarity NPC42171
0.5484 Remote Similarity NPC287885
0.5455 Remote Similarity NPC86020
0.5424 Remote Similarity NPC274200
0.5391 Remote Similarity NPC224314
0.5385 Remote Similarity NPC265275
0.5378 Remote Similarity NPC156789
0.5294 Remote Similarity NPC300557
0.5259 Remote Similarity NPC113044
0.5259 Remote Similarity NPC283829
0.5259 Remote Similarity NPC161676
0.5169 Remote Similarity NPC197231
0.5167 Remote Similarity NPC6806
0.5126 Remote Similarity NPC602423
0.512 Remote Similarity NPC160084
0.512 Remote Similarity NPC473474
0.5115 Remote Similarity NPC477808
0.5079 Remote Similarity NPC486383

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC486386 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
0.5739 Remote Similarity NPD8449 Approved

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