Natural Product: NPC118995

Natural Product IDNPC118995
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
OFWRPYLODPDMMJ-XZMWWMHISA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 10102851
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 OFWRPYLODPDMMJ-XZMWWMHISA-N
Standard InCHI InChI=1S/C57H94O27/c1-21-8-13-57(73-20-21)22(2)34-29(84-57)15-28-26-7-6-24-14-25(9-11-55(24,4)27(26)10-12-56(28,34)5)75-51-44(71)40(67)47(33(19-61)78-51)81-54-49(48(37(64)31(17-59)77-54)82-52-43(70)39(66)36(63)30(16-58)76-52)83-53-45(72)41(68)46(32(18-60)79-53)80-50-42(69)38(65)35(62)23(3)74-50/h21-54,58-72H,6-20H2,1-5H3/t21-,22+,23+,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-,52+,53+,54+,55+,56+,57-/m1/s1
SMILES C[C@@H]1CC[C@@]2([C@@H](C)C3C(C[C@H]4[C@@H]5CC[C@H]6C[C@H](CC[C@]6(C)[C@H]5CC[C@]34C)O[C@H]3[C@@H]([C@H]([C@H]([C@@H](CO)O3)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O[C@H]3[C@@H]([C@@H]([C@H]([C@H](C)O3)O)O)O)O)O)O)O)O2)OC1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1210.6 Volume:   1137.643
?
Van der Waals volume.
Dense:   1.064 LogP:   0.645
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.454
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.879
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   14.0 Rigid Bonds:   60.0
TPSA:   414.21
?
Topological Polar Surface Area.
H-Bond Acceptor:   27.0
H-Bond Donor:   15.0 Rings:   11.0
Heavy Atoms:   27.0

MedChem Properties

QED Drug-Likeness Score:   0.074 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.606 Fsp3:   1.0
MCE-18:   292.0
?
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:   0.657 Fluc inhibitor:   0.223
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.005
?
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:   0.408 Promiscuous compounds:   0.061

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.027 MDCK Permeability:   -4.941
Pgp-inhibitor:   0.0 Pgp-substrate:   0.7
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):   0.432
20% Bioavailability (F20%):   0.238 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.002 MRP1:   0.007
Plasma Protein Binding (PPB):   36.517% Volume Distribution (VD):   -0.389
Fu: 45.52%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.001
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   1.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.871
HLM stability:   0.043
?
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):  -0.797 Half-life (T1/2):  3.899

ADMET: Toxicity

hERG Blockers:  0.003 hERG Blockers (10um):  0.003
Human Hepatotoxicity (H-HT):  0.646 Drug-induced Liver Injury (DILI):  0.997
AMES Toxicity:  0.997 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.019 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.692 Drug-induced Nephrotoxicity:  0.978
Genotoxicity:  0.003 RPMI-8226 Immunitoxicity:  0.394
A549 Cytotoxicity:  0.995 Hek293 Cytotoxicity:  0.964
BCF:   1.392
?
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:   3.33
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.378
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.613
?
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
NPO7928 Agave east-one Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7928 Agave east-one Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7928 Agave east-one Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]

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

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 NPC118995 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
0.8936 High Similarity NPC97700
0.8936 High Similarity NPC184617
0.8936 High Similarity NPC30856
0.875 High Similarity NPC206003
0.875 High Similarity NPC473610
0.8506 High Similarity NPC325828
0.8317 Intermediate Similarity NPC132080
0.8105 Intermediate Similarity NPC475351
0.81 Intermediate Similarity NPC116756
0.8065 Intermediate Similarity NPC107962
0.802 Intermediate Similarity NPC232037
0.7941 Intermediate Similarity NPC470864
0.7864 Intermediate Similarity NPC83137
0.7789 Intermediate Similarity NPC6295
0.7619 Intermediate Similarity NPC233433
0.7604 Intermediate Similarity NPC125324
0.757 Intermediate Similarity NPC470866
0.7549 Intermediate Similarity NPC115165
0.7474 Intermediate Similarity NPC19400
0.7447 Intermediate Similarity NPC250393
0.734 Intermediate Similarity NPC477451
0.7292 Intermediate Similarity NPC107188
0.7255 Intermediate Similarity NPC300557
0.7234 Intermediate Similarity NPC234352
0.7143 Intermediate Similarity NPC220836
0.713 Intermediate Similarity NPC477811
0.7128 Intermediate Similarity NPC297348
0.7128 Intermediate Similarity NPC249204
0.7128 Intermediate Similarity NPC48339
0.7128 Intermediate Similarity NPC141769
0.7128 Intermediate Similarity NPC477547
0.7087 Intermediate Similarity NPC51172
0.7087 Intermediate Similarity NPC49032
0.7075 Intermediate Similarity NPC475625
0.7059 Intermediate Similarity NPC602423
0.7037 Intermediate Similarity NPC476112
0.7037 Intermediate Similarity NPC307534
0.6961 Remote Similarity NPC473601
0.6916 Remote Similarity NPC473518
0.6887 Remote Similarity NPC475319
0.6875 Remote Similarity NPC94086
0.6875 Remote Similarity NPC473817
0.6852 Remote Similarity NPC232611
0.6827 Remote Similarity NPC92890
0.6765 Remote Similarity NPC160426
0.6737 Remote Similarity NPC485594
0.6733 Remote Similarity NPC470432
0.6733 Remote Similarity NPC230507
0.6727 Remote Similarity NPC470862
0.6667 Remote Similarity NPC195297
0.6636 Remote Similarity NPC98018
0.6636 Remote Similarity NPC284104
0.6636 Remote Similarity NPC103616
0.6607 Remote Similarity NPC31896
0.66 Remote Similarity NPC211354
0.6569 Remote Similarity NPC485595
0.656 Remote Similarity NPC481189
0.6514 Remote Similarity NPC470863
0.6466 Remote Similarity NPC477807
0.6455 Remote Similarity NPC309278
0.6452 Remote Similarity NPC329807
0.6389 Remote Similarity NPC128572
0.6378 Remote Similarity NPC329727
0.6355 Remote Similarity NPC477809
0.6296 Remote Similarity NPC471464
0.6296 Remote Similarity NPC6806
0.626 Remote Similarity NPC481190
0.6239 Remote Similarity NPC480555
0.6239 Remote Similarity NPC150372
0.6238 Remote Similarity NPC222731
0.6228 Remote Similarity NPC84111
0.6228 Remote Similarity NPC287483
0.6228 Remote Similarity NPC470865
0.6218 Remote Similarity NPC210569
0.6111 Remote Similarity NPC475643
0.61 Remote Similarity NPC177834
0.6091 Remote Similarity NPC151134
0.6068 Remote Similarity NPC470867
0.6068 Remote Similarity NPC262050
0.6053 Remote Similarity NPC108072
0.604 Remote Similarity NPC294686
0.6 Remote Similarity NPC477808
0.5963 Remote Similarity NPC470433
0.5963 Remote Similarity NPC46190
0.5963 Remote Similarity NPC171073
0.5952 Remote Similarity NPC330026
0.5948 Remote Similarity NPC480553
0.5929 Remote Similarity NPC269297
0.5929 Remote Similarity NPC222202
0.5917 Remote Similarity NPC473505
0.5865 Remote Similarity NPC121453
0.5846 Remote Similarity NPC329820
0.5842 Remote Similarity NPC181845
0.5833 Remote Similarity NPC113044
0.5833 Remote Similarity NPC283829
0.5833 Remote Similarity NPC14704
0.5833 Remote Similarity NPC161676
0.5812 Remote Similarity NPC92297
0.5806 Remote Similarity NPC305771
0.5806 Remote Similarity NPC94072
0.5806 Remote Similarity NPC169816
0.5776 Remote Similarity NPC480554
0.57 Remote Similarity NPC24960
0.568 Remote Similarity NPC263359
0.5607 Remote Similarity NPC264101
0.5603 Remote Similarity NPC475333
0.5603 Remote Similarity NPC32361
0.5603 Remote Similarity NPC224098
0.5603 Remote Similarity NPC208383
0.56 Remote Similarity NPC473774
0.56 Remote Similarity NPC481419
0.56 Remote Similarity NPC481417
0.5565 Remote Similarity NPC51520
0.5565 Remote Similarity NPC15918
0.5565 Remote Similarity NPC303069
0.5556 Remote Similarity NPC194207
0.5556 Remote Similarity NPC22779
0.5517 Remote Similarity NPC475550
0.5487 Remote Similarity NPC248746
0.5484 Remote Similarity NPC273002
0.547 Remote Similarity NPC470861
0.5455 Remote Similarity NPC141433
0.5447 Remote Similarity NPC480556
0.5433 Remote Similarity NPC244431
0.5403 Remote Similarity NPC224314
0.54 Remote Similarity NPC277715
0.5328 Remote Similarity NPC232054
0.5327 Remote Similarity NPC474399
0.5317 Remote Similarity NPC79900
0.531 Remote Similarity NPC202898
0.5304 Remote Similarity NPC274200
0.53 Remote Similarity NPC144790
0.53 Remote Similarity NPC149400
0.5294 Remote Similarity NPC481420
0.5294 Remote Similarity NPC481421
0.525 Remote Similarity NPC92710
0.5229 Remote Similarity NPC54619
0.5214 Remote Similarity NPC294129
0.5214 Remote Similarity NPC102016
0.5214 Remote Similarity NPC95051
0.521 Remote Similarity NPC13193
0.5172 Remote Similarity NPC42171
0.5135 Remote Similarity NPC215408
0.5091 Remote Similarity NPC306131
0.5091 Remote Similarity NPC200802
0.5044 Remote Similarity NPC70204
0.5043 Remote Similarity NPC249553

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC118995 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
0.8506 High Similarity NPD8171 Phase 2
0.7245 Intermediate Similarity NPD8170 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