Structure

Physi-Chem Properties

Molecular Weight:  769.37
Volume:  773.815
LogP:  3.756
LogD:  2.632
LogS:  -4.681
# Rotatable Bonds:  16
TPSA:  173.57
# H-Bond Aceptor:  14
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  14

MedChem Properties

QED Drug-Likeness Score:  0.142
Synthetic Accessibility Score:  6.54
Fsp3:  0.659
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.335
MDCK Permeability:  0.00020947775919921696
Pgp-inhibitor:  1.0
Pgp-substrate:  0.998
Human Intestinal Absorption (HIA):  0.302
20% Bioavailability (F20%):  0.084
30% Bioavailability (F30%):  0.881

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.016
Plasma Protein Binding (PPB):  72.15116882324219%
Volume Distribution (VD):  2.51
Pgp-substrate:  21.459976196289062%

ADMET: Metabolism

CYP1A2-inhibitor:  0.01
CYP1A2-substrate:  0.013
CYP2C19-inhibitor:  0.013
CYP2C19-substrate:  0.12
CYP2C9-inhibitor:  0.068
CYP2C9-substrate:  0.021
CYP2D6-inhibitor:  0.862
CYP2D6-substrate:  0.089
CYP3A4-inhibitor:  0.537
CYP3A4-substrate:  0.772

ADMET: Excretion

Clearance (CL):  3.608
Half-life (T1/2):  0.111

ADMET: Toxicity

hERG Blockers:  0.186
Human Hepatotoxicity (H-HT):  0.982
Drug-inuced Liver Injury (DILI):  0.962
AMES Toxicity:  0.027
Rat Oral Acute Toxicity:  0.36
Maximum Recommended Daily Dose:  0.942
Skin Sensitization:  0.158
Carcinogencity:  0.017
Eye Corrosion:  0.003
Eye Irritation:  0.013
Respiratory Toxicity:  0.938

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General Info & Identifiers & Properties  
Structure MOL file  
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Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC28705

Natural Product ID:  NPC28705
Common Name*:   NCVLHUMLSYFYEW-QJRDYPDMSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NCVLHUMLSYFYEW-QJRDYPDMSA-N
Standard InCHI:  InChI=1S/C41H55NO13/c1-21-30(50-22(2)43)17-28-35(52-24(4)45)37-40(9,38(54-26(6)47)36(53-25(5)46)34(21)39(28,7)8)31(51-23(3)44)19-32(41(37)20-49-41)55-33(48)18-29(42(10)11)27-15-13-12-14-16-27/h12-16,28-32,35-38H,17-20H2,1-11H3/t28-,29+,30-,31-,32-,35+,36+,37-,38-,40+,41-/m0/s1
SMILES:  CC1=C2[C@H]([C@@H]([C@]3(C)[C@H](C[C@@H]([C@@]4(CO4)[C@H]3[C@@H]([C@H](C[C@@H]1OC(=O)C)C2(C)C)OC(=O)C)OC(=O)C[C@H](c1ccccc1)N(C)C)OC(=O)C)OC(=O)C)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5319245
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0000676] Taxanes and derivatives

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO27746 Taxus mairei Species Taxaceae Eukaryota stem bark n.a. n.a. PMID[11473432]
NPO25366 Sapium indicum Species Euphorbiaceae Eukaryota Fruits n.a. n.a. PMID[12713411]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[16124776]
NPO6645.1 Picea jezoensis var. jezoensis Varieties Pinaceae Eukaryota bark n.a. n.a. PMID[17907781]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[18804027]
NPO6645.1 Picea jezoensis var. jezoensis Varieties Pinaceae Eukaryota bark n.a. n.a. PMID[19646881]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[20233596]
NPO25054 Phaleria macrocarpa Species Thymelaeaceae Eukaryota nut shell n.a. n.a. PMID[23044367]
NPO25252 Nannocystis exedens Species Nannocystaceae Bacteria n.a. n.a. n.a. PMID[24460410]
NPO25311 Guettarda platypoda Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[2553871]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[32058711]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[8557595]
NPO27746 Taxus mairei Species Taxaceae Eukaryota Roots n.a. n.a. PMID[8991951]
NPO27746 Taxus mairei Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[9644081]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24373 Lobelia inflata Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24373 Lobelia inflata Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23788 Beauveria bassiana Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24852 Helicia nilagirica Species Proteaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22283 Alhagi maurorum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27746 Taxus mairei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30249 Taxus malrei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15482 Vanderbylia fraxinea Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28460 Achyrocline tomentosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22152 Tecoma undulata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24566 Marasmiellus ramealis Species Omphalotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25389 Allium angulosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25466 Lecanora sulphurella Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22283 Alhagi maurorum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25492 Botryllus leachi Species Styelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23994 Ormosia macrophylla Species Limoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18706 Anemone thalictroides Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24373 Lobelia inflata Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23894 Pulicaria insignis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25054 Phaleria macrocarpa Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22618 Psolus eximius Species Psolidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14189 Osmundaria spiralis Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25311 Guettarda platypoda Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24461 Clusia sandiensis Species Clusiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25366 Sapium indicum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24607 Goniothalamus dolichocarpus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24852 Helicia nilagirica Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3721 Achyranthes obtusifolia Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24278 Pistacia chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24882 Erythrophleum chlorostachys Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6645.1 Picea jezoensis var. jezoensis Varieties Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27390 Vernonia brevifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27746 Taxus mairei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25252 Nannocystis exedens Species Nannocystaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO24802 Diploprion bifasciatum Species Serranidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24730 Lactarius deliciosus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25277 Seiridium cupressi Species Sporocadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20264 Moonia heterophylla n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO25441 Desmodium pulchellu Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23788 Beauveria bassiana Species Cordycipitaceae 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 NP ID 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

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

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC28705 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC28705 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage

  Bioactivity similarity: Similar Natural Products in NPASS

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