NPASS Compound

Structure

NPC226981 OpenBabel06302216202D 28 31 0 0 1 0 0 0 0 0999 V2000 3.2805 -3.9911 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3065 -3.9914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8198 -4.8350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8193 -3.1480 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3061 -2.3043 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8188 -1.4610 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8448 -1.4613 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3581 -2.3049 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8445 -0.4873 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6876 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6873 0.9749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9744 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8448 1.4617 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8451 2.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6896 2.9239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5339 2.4362 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3779 2.9234 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2215 2.4357 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2212 1.4607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3773 0.9734 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5336 1.4612 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5333 0.4612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6891 0.9739 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6888 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8443 -0.4877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0003 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0878 2.9353 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 1 0 0 0 9 7 1 1 0 0 0 9 10 1 0 0 0 0 9 26 1 0 0 0 0 10 11 1 0 0 0 0 12 11 1 6 0 0 0 12 13 1 0 0 0 0 12 26 1 0 0 0 0 13 14 1 1 0 0 0 13 23 1 0 0 0 0 14 15 1 0 0 0 0 16 15 1 6 0 0 0 16 17 1 0 0 0 0 16 21 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 18 28 1 6 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 6 0 0 0 21 23 1 0 0 0 0 23 24 1 6 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	388.37
Volume:	450.112
LogP:	8.042
LogD:	6.555
LogS:	-6.831
# Rotatable Bonds:	5
TPSA:	20.23
# H-Bond Aceptor:	1
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.518
Synthetic Accessibility Score:	4.148
Fsp3:	1.0
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.654
MDCK Permeability:	8.840444024826866e-06
Pgp-inhibitor:	0.946
Pgp-substrate:	0.254
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.998
30% Bioavailability (F30%):	0.938

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.232
Plasma Protein Binding (PPB):	95.17621612548828%
Volume Distribution (VD):	1.42
Pgp-substrate:	1.4506269693374634%

ADMET: Metabolism

CYP1A2-inhibitor:	0.171
CYP1A2-substrate:	0.186
CYP2C19-inhibitor:	0.128
CYP2C19-substrate:	0.812
CYP2C9-inhibitor:	0.34
CYP2C9-substrate:	0.085
CYP2D6-inhibitor:	0.029
CYP2D6-substrate:	0.093
CYP3A4-inhibitor:	0.442
CYP3A4-substrate:	0.285

ADMET: Excretion

Clearance (CL):	11.913
Half-life (T1/2):	0.061

ADMET: Toxicity

hERG Blockers:	0.993
Human Hepatotoxicity (H-HT):	0.19
Drug-inuced Liver Injury (DILI):	0.813
AMES Toxicity:	0.019
Rat Oral Acute Toxicity:	0.021
Maximum Recommended Daily Dose:	0.192
Skin Sensitization:	0.982
Carcinogencity:	0.226
Eye Corrosion:	0.997
Eye Irritation:	0.882
Respiratory Toxicity:	0.779

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC226981

Natural Product ID:	NPC226981
*Common Name:**	QYIXCDOBOSTCEI-ILFYRDGGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QYIXCDOBOSTCEI-ILFYRDGGSA-N
Standard InCHI:	InChI=1S/C27H48O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h18-25,28H,6-17H2,1-5H3/t19-,20+,21+,22+,23+,24+,25+,26+,27-/m1/s1
SMILES:	CC(C)CCC[C@@H](C)[C@@H]1CC[C@H]2[C@@H]3CC[C@H]4C[C@H](CC[C@]4(C)[C@H]3CC[C@]12C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0003566] Cholestane steroids [CHEMONTID:0001469] Cholesterols 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
NPO17673	Dysidea herbacea	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[10075800]
NPO17673	Dysidea herbacea	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[10650102]
NPO17673	Dysidea herbacea	Species	n.a.	n.a.	n.a.	Mandapam Coast, Tamilnadu, India	n.a.	PMID[22704923]
NPO17673	Dysidea herbacea	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[9463111]
NPO13746	Achillea leptophylla	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4863	Dioscorea futschauensis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4863	Dioscorea futschauensis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13746	Achillea leptophylla	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16323	Umbilicaria proboscidea	Species	Umbilicariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4863	Dioscorea futschauensis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4863	Dioscorea futschauensis	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13746	Achillea leptophylla	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13321	Viguiera cordifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1793	Uvaria mocoli	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17210	Dorstenia barnimiana	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9044	Rubia ustulata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13985	Oxybasis urbica	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16204	Zieria chevalieri	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17991	Sedum forsterianum	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7857	Verbascum georgicum	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16323	Umbilicaria proboscidea	Species	Umbilicariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16684	Alibertia macrophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17673	Dysidea herbacea	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO4863	Dioscorea futschauensis	Species	Dioscoreaceae	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 NPC226981 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	370
0.1-0.2	5106
0.2-0.3	18145
0.3-0.4	7880
0.4-0.5	4813
0.5-0.6	4053
0.6-0.7	1654
0.7-0.8	475
0.8-0.85	133
0.85-0.9	49
0.9-0.95	13
0.95-1	6

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 NPC226981 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	383
0.1-0.2	4541
0.2-0.3	3071
0.3-0.4	657
0.4-0.5	205
0.5-0.6	192
0.6-0.7	66
0.7-0.8	15
0.8-0.85	14
0.85-0.9	6
0.9-0.95	0
0.95-1	0

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