NPASS Compound

Structure

NPC11977 OpenBabel06302215112D 47 51 0 0 1 0 0 0 0 0999 V2000 2.6929 -1.3602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9656 -1.9904 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1561 -1.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7564 -0.5948 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8933 0.3576 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5235 1.0849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4468 1.3560 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3701 1.0849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8903 1.8944 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0002 0.3576 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.1371 -0.5948 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0931 -0.7045 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.7438 0.0044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6831 -0.2046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9717 -1.1226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.3337 0.5043 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0451 1.4223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6958 2.1312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6351 1.9222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9237 1.0043 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2730 0.2953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2842 -1.6476 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.1595 -2.0474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4463 -2.1208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7374 -1.4701 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.9279 -1.9904 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1990 -2.9137 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0529 -0.7938 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1249 -1.0485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6380 -2.9104 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4404 -0.3721 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7508 1.1571 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8423 2.1150 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0584 2.6732 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7176 2.5148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4468 2.3182 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6134 2.7994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7801 2.3182 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6134 3.7616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4468 4.2428 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4468 5.2050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6134 5.6862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7801 5.2050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7801 4.2428 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8933 -0.3576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7564 0.5948 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 26 1 0 0 0 0 2 3 2 0 0 0 0 4 3 1 6 0 0 0 4 5 1 0 0 0 0 4 45 1 0 0 0 0 5 6 1 0 0 0 0 5 45 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 7 36 1 1 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 10 32 1 0 0 0 0 11 12 1 0 0 0 0 11 25 1 0 0 0 0 12 13 1 1 0 0 0 12 22 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 16 1 0 0 0 0 16 21 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 22 23 1 1 0 0 0 22 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 25 28 1 0 0 0 0 26 27 2 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 29 31 1 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 36 37 1 0 0 0 0 37 38 2 0 0 0 0 37 39 1 0 0 0 0 39 44 2 0 0 0 0 39 40 1 0 0 0 0 40 41 2 0 0 0 0 41 42 1 0 0 0 0 42 43 2 0 0 0 0 43 44 1 0 0 0 0 45 46 1 0 0 0 0 45 47 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	640.3
Volume:	676.365
LogP:	5.539
LogD:	3.856
LogS:	-4.829
# Rotatable Bonds:	10
TPSA:	113.04
# H-Bond Aceptor:	8
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.142
Synthetic Accessibility Score:	5.455
Fsp3:	0.462
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
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:	-4.944
MDCK Permeability:	3.388491677469574e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.014
20% Bioavailability (F20%):	0.033
30% Bioavailability (F30%):	0.356

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.015
Plasma Protein Binding (PPB):	98.17240142822266%
Volume Distribution (VD):	1.845
Pgp-substrate:	4.293286323547363%

ADMET: Metabolism

CYP1A2-inhibitor:	0.086
CYP1A2-substrate:	0.072
CYP2C19-inhibitor:	0.743
CYP2C19-substrate:	0.07
CYP2C9-inhibitor:	0.959
CYP2C9-substrate:	0.084
CYP2D6-inhibitor:	0.083
CYP2D6-substrate:	0.041
CYP3A4-inhibitor:	0.866
CYP3A4-substrate:	0.598

ADMET: Excretion

Clearance (CL):	4.003
Half-life (T1/2):	0.205

ADMET: Toxicity

hERG Blockers:	0.037
Human Hepatotoxicity (H-HT):	0.973
Drug-inuced Liver Injury (DILI):	0.984
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.963
Maximum Recommended Daily Dose:	0.838
Skin Sensitization:	0.022
Carcinogencity:	0.174
Eye Corrosion:	0.003
Eye Irritation:	0.036
Respiratory Toxicity:	0.94

Download Data

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

Natural Product: NPC11977

Natural Product ID:	NPC11977
*Common Name:**	VBGBQNWVGHQTSW-HNVQZHRISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VBGBQNWVGHQTSW-HNVQZHRISA-N
Standard InCHI:	InChI=1S/C39H44O8/c1-22-18-30-31(38(30,6)7)20-33(46-37(44)28-16-12-9-13-17-28)24(3)35(45-25(4)40)34-29(19-32(42)27-14-10-8-11-15-27)23(2)21-39(34,36(22)43)47-26(5)41/h8-18,23,29-31,33-35H,3,19-21H2,1-2,4-7H3/b22-18+/t23-,29-,30-,31-,33+,34+,35-,39+/m0/s1
SMILES:	C/C/1=C[C@H]2[C@H](C[C@H](C(=C)[C@@H]([C@H]3[C@@H](CC(=O)c4ccccc4)[C@@H](C)C[C@@]3(C1=O)OC(=O)C)OC(=O)C)OC(=O)c1ccccc1)C2(C)C
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
NPO520	Euphorbia lathyris	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12542364]
NPO10036	Bruguiera cylindrica	Species	Rhizophoraceae	Eukaryota	Fruits	n.a.	n.a.	PMID[15165157]
NPO2462	Machilus robusta	Species	Lauraceae	Eukaryota	bark	n.a.	n.a.	PMID[21627109]
NPO2462	Machilus robusta	Species	Lauraceae	Eukaryota	n.a.	bark	n.a.	PMID[21627109]
NPO520	Euphorbia lathyris	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30817151]
NPO520	Euphorbia lathyris	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4235	Thymus magnus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9866	Symphytum tuberosum	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO520	Euphorbia lathyris	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9866	Symphytum tuberosum	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4235	Thymus magnus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO520	Euphorbia lathyris	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO520	Euphorbia lathyris	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO5571	Jacobaea arnautorum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4494	Ecbolium linneanum	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8283	Pseudophegopteris subaurita	Species	Thelypteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10733	Plantago uniflora	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2462	Machilus robusta	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10036	Bruguiera cylindrica	Species	Rhizophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9866	Symphytum tuberosum	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10479	Ophiocoma echinata	Species	Ophiocomidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3940	Erioderma chilense	Species	Pannariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4235	Thymus magnus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10959	Kalanchoe marmorata	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1000	Thymus transcaucasicus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10833	Heteromma simplicifolium	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO520	Euphorbia lathyris	Species	Euphorbiaceae	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 NPC11977 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	333
0.1-0.2	1286
0.2-0.3	2319
0.3-0.4	6136
0.4-0.5	12085
0.5-0.6	13272
0.6-0.7	6380
0.7-0.8	709
0.8-0.85	62
0.85-0.9	82
0.9-0.95	28
0.95-1	5

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 NPC11977 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	276
0.1-0.2	836
0.2-0.3	1464
0.3-0.4	2924
0.4-0.5	2322
0.5-0.6	1065
0.6-0.7	249
0.7-0.8	14
0.8-0.85	0
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