NPASS Compound

Structure

NPC30250 OpenBabel06302215282D 46 51 0 0 1 0 0 0 0 0999 V2000 -1.8171 4.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6831 4.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 4.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6831 3.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8171 2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8171 1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6831 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4152 3.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4152 1.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6831 0.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5491 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 -0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 -1.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6831 -1.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8171 -1.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3171 -2.0570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8171 -1.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8171 -0.1910 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9511 0.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9511 1.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 1.6180 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5878 0.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0878 1.6750 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5878 2.5411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0878 1.6750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5878 0.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0878 -0.0570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5878 -0.9230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0878 -0.0570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0878 1.6750 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.0878 1.6750 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.0878 1.6750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5878 2.5411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0878 3.4071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0878 3.4071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5878 2.5411 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.4538 3.0411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4538 2.0411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3198 2.5411 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4538 1.0411 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 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 9 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 12 1 0 0 0 0 8 9 1 0 0 0 0 8 11 1 0 0 0 0 9 10 1 0 0 0 0 12 20 1 0 0 0 0 12 13 1 1 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 20 17 1 1 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 21 46 1 6 0 0 0 22 6 1 1 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 1 0 0 0 24 46 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 1 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 30 29 1 6 0 0 0 30 31 1 0 0 0 0 30 36 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 33 34 1 0 0 0 0 35 34 1 6 0 0 0 35 36 1 0 0 0 0 35 41 1 0 0 0 0 36 37 1 6 0 0 0 36 38 1 0 0 0 0 38 39 1 0 0 0 0 39 40 1 0 0 0 0 40 41 1 0 0 0 0 41 42 1 1 0 0 0 41 43 1 0 0 0 0 43 44 2 0 0 0 0 43 45 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	636.44
Volume:	688.616
LogP:	8.482
LogD:	5.456
LogS:	-4.057
# Rotatable Bonds:	7
TPSA:	96.22
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	6
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.204
Synthetic Accessibility Score:	5.54
Fsp3:	0.775
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.251
MDCK Permeability:	1.5897689081612043e-05
Pgp-inhibitor:	0.861
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.78
30% Bioavailability (F30%):	0.798

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.22
Plasma Protein Binding (PPB):	97.66539764404297%
Volume Distribution (VD):	0.481
Pgp-substrate:	3.141986608505249%

ADMET: Metabolism

CYP1A2-inhibitor:	0.012
CYP1A2-substrate:	0.666
CYP2C19-inhibitor:	0.039
CYP2C19-substrate:	0.797
CYP2C9-inhibitor:	0.191
CYP2C9-substrate:	0.796
CYP2D6-inhibitor:	0.121
CYP2D6-substrate:	0.151
CYP3A4-inhibitor:	0.284
CYP3A4-substrate:	0.327

ADMET: Excretion

Clearance (CL):	2.273
Half-life (T1/2):	0.017

ADMET: Toxicity

hERG Blockers:	0.032
Human Hepatotoxicity (H-HT):	0.286
Drug-inuced Liver Injury (DILI):	0.035
AMES Toxicity:	0.024
Rat Oral Acute Toxicity:	0.705
Maximum Recommended Daily Dose:	0.971
Skin Sensitization:	0.922
Carcinogencity:	0.101
Eye Corrosion:	0.003
Eye Irritation:	0.318
Respiratory Toxicity:	0.906

Download Data

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

Natural Product: NPC30250

Natural Product ID:	NPC30250
*Common Name:**	XWJQKJGYCVQLON-RBZLTNCOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XWJQKJGYCVQLON-RBZLTNCOSA-N
Standard InCHI:	InChI=1S/C40H60O6/c1-22(2)25-21-26-30(32(42)31(25)41)40(9)19-10-16-37(5,6)35(40)34-33(26)45-29(46-34)20-23(3)12-14-27-24(4)13-15-28-38(27,7)17-11-18-39(28,8)36(43)44/h21-23,27-29,33-35,41-42H,4,10-20H2,1-3,5-9H3,(H,43,44)/t23-,27-,28+,29+,33+,34-,35-,38+,39-,40+/m0/s1
SMILES:	CC(C)c1cc2c(c(c1O)O)[C@@]1(C)CCCC(C)(C)[C@@H]1[C@@H]1[C@@H]2O[C@@H](C[C@@H](C)CC[C@H]2C(=C)CC[C@@H]3[C@]2(C)CCC[C@]3(C)C(=O)O)O1
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:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

*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
NPO13135	Campylotropis hirtella	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19481938]
NPO12796	Periploca sepium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28294615]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31291099]
NPO7773	Crinum moorei	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12796	Periploca sepium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13135	Campylotropis hirtella	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6731	Ononis spinosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12796	Periploca sepium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6731	Ononis spinosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7773	Crinum moorei	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13135	Campylotropis hirtella	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12796	Periploca sepium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6731	Ononis spinosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12796	Periploca sepium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12205	Eucalyptus apodophylla	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5043	Eria japonica	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11576	Glycosmis macrophylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8934	Gypsophila perfoliata	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10605	Tristania conferta	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9532	Vernonia cistifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22691	Mentha cardiaca	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13135	Campylotropis hirtella	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6289	Ceropegia dichotoma	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5456	Juniperus drupacea	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1815	Breonia chinensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7773	Crinum moorei	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9704	Sonneratia caseolaris	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1257	Distephanus angulifolius	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23384	Rhodiola semenovii	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12796	Periploca sepium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9319	Pterocaulon virgatum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10638	Plectranthus myrianthus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21720	Talaromyces variabilis	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3873	Crotalaria candicans	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7822.1	Eucalyptus globulus subsp. bicostata	Subspecies	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11843	Stephania zippeliana	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12565	Hypericum polyanthemum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12091	Martensia denticulata	Species	Delesseriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11190	Veronica polita	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO526	Salvia sessei	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10922	Pentaclethra macrophylla	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6731	Ononis spinosa	Species	Fabaceae	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 NPC30250 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	346
0.1-0.2	1377
0.2-0.3	2826
0.3-0.4	5350
0.4-0.5	9523
0.5-0.6	10647
0.6-0.7	10040
0.7-0.8	2454
0.8-0.85	119
0.85-0.9	13
0.9-0.95	2
0.95-1	0

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 NPC30250 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	292
0.1-0.2	811
0.2-0.3	1691
0.3-0.4	2777
0.4-0.5	2149
0.5-0.6	1076
0.6-0.7	310
0.7-0.8	42
0.8-0.85	2
0.85-0.9	0
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