NPASS Compound

Structure

NPC307248 OpenBabel06302215532D 55 61 0 0 1 0 0 0 0 0999 V2000 9.3726 -1.4758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3726 -0.4919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.2247 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.5206 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6685 -0.4919 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.6685 -1.4758 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.8165 -1.9677 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9644 -1.4758 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9644 -0.4919 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.8165 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.8165 0.9839 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1123 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2603 -0.4919 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2603 -1.4758 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4082 -1.9677 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5562 -1.4758 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5562 -0.4919 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4082 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4082 0.9839 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7041 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8521 -0.4919 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8521 -1.4758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.9677 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8521 -1.4758 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8521 -2.4597 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8521 -0.4919 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7041 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5562 -0.4919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5562 -1.4758 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2603 -0.4919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7041 -1.9677 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7041 -2.9516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5562 -3.4435 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4082 -2.9516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2603 -3.4435 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2603 -4.4274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1123 -4.9194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6043 -5.7714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6204 -5.7714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9644 -4.4274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9644 -3.4435 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1123 -2.9516 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1123 -1.9677 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2603 -1.4758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4082 -1.9677 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4082 -0.9839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9644 -2.4597 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9644 -1.4758 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8165 -2.9516 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4919 0.8521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4919 0.8521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4758 0.8521 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1123 -1.9677 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.5206 -1.9677 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 10 1 0 0 0 0 6 7 1 0 0 0 0 6 55 1 6 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 9 12 1 1 0 0 0 10 11 1 6 0 0 0 13 12 1 1 0 0 0 13 14 1 0 0 0 0 13 18 1 0 0 0 0 14 15 1 0 0 0 0 14 54 1 1 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 20 1 1 0 0 0 18 19 1 6 0 0 0 21 20 1 1 0 0 0 21 22 1 0 0 0 0 21 50 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 31 1 0 0 0 0 24 25 1 1 0 0 0 24 26 1 0 0 0 0 26 27 1 1 0 0 0 26 50 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 45 1 0 0 0 0 29 30 1 1 0 0 0 29 31 1 0 0 0 0 31 32 1 1 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 34 45 1 0 0 0 0 34 35 1 0 0 0 0 35 36 1 6 0 0 0 35 42 1 0 0 0 0 36 37 1 0 0 0 0 37 38 1 0 0 0 0 37 39 1 0 0 0 0 37 40 1 0 0 0 0 40 41 1 0 0 0 0 41 42 1 0 0 0 0 42 43 1 0 0 0 0 42 47 1 1 0 0 0 43 44 1 0 0 0 0 44 45 1 0 0 0 0 45 46 1 6 0 0 0 47 48 2 0 0 0 0 47 49 1 0 0 0 0 50 51 1 1 0 0 0 50 52 1 0 0 0 0 52 53 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	788.47
Volume:	816.721
LogP:	4.591
LogD:	2.163
LogS:	-2.755
# Rotatable Bonds:	30
TPSA:	256.18
# H-Bond Aceptor:	16
# H-Bond Donor:	8
# Rings:	1
# Heavy Atoms:	16

MedChem Properties

QED Drug-Likeness Score:	0.038
Synthetic Accessibility Score:	4.664
Fsp3:	0.65
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:	-6.443
MDCK Permeability:	0.00015939523291308433
Pgp-inhibitor:	0.244
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.891
20% Bioavailability (F20%):	0.95
30% Bioavailability (F30%):	0.912

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.058
Plasma Protein Binding (PPB):	42.88846206665039%
Volume Distribution (VD):	0.514
Pgp-substrate:	28.573490142822266%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.001
CYP2C19-inhibitor:	0.033
CYP2C19-substrate:	0.033
CYP2C9-inhibitor:	0.021
CYP2C9-substrate:	0.982
CYP2D6-inhibitor:	0.094
CYP2D6-substrate:	0.053
CYP3A4-inhibitor:	0.083
CYP3A4-substrate:	0.008

ADMET: Excretion

Clearance (CL):	1.19
Half-life (T1/2):	0.877

ADMET: Toxicity

hERG Blockers:	0.001
Human Hepatotoxicity (H-HT):	0.992
Drug-inuced Liver Injury (DILI):	0.835
AMES Toxicity:	0.002
Rat Oral Acute Toxicity:	0.04
Maximum Recommended Daily Dose:	0.669
Skin Sensitization:	0.138
Carcinogencity:	0.073
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.838

Download Data

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

Natural Product: NPC307248

Natural Product ID:	NPC307248
*Common Name:**	BZYPXVLQGFSNFQ-FVYHMAAWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BZYPXVLQGFSNFQ-FVYHMAAWSA-N
Standard InCHI:	InChI=1S/C42H66O13/c1-22(44)53-32-25(45)19-52-35(30(32)47)55-33-26(46)20-51-34(31(33)48)54-29-11-12-38(4)27(39(29,5)21-43)10-13-41(7)28(38)9-8-23-24-18-37(2,3)14-16-42(24,36(49)50)17-15-40(23,41)6/h8,24-35,43,45-48H,9-21H2,1-7H3,(H,49,50)/t24-,25+,26-,27+,28+,29-,30+,31+,32-,33-,34-,35-,38-,39-,40+,41+,42-/m0/s1
SMILES:	CC(=O)O[C@H]1[C@@H](CO[C@H]([C@@H]1O)O[C@H]1[C@H](CO[C@H]([C@@H]1O)O[C@H]1CC[C@@]2(C)[C@@H](CC[C@]3(C)[C@@H]2CC=C2[C@@H]4CC(C)(C)CC[C@@]4(CC[C@@]32C)C(=O)O)[C@]1(C)CO)O)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:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO11357	Nephelium lappaceum	Species	Sapindaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[16180821]
NPO5258	Fagara zanthoxyloides	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[22472691]
NPO21322	Plinia cauliflora	Species	Myrtaceae	Eukaryota	leaves	n.a.	n.a.	PMID[32706260]
NPO11357	Nephelium lappaceum	Species	Sapindaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO358	Uncaria guianensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4307	Canarium album	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO358	Uncaria guianensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4307	Canarium album	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4307	Canarium album	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4307	Canarium album	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1933	Sideritis nutans	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO358	Uncaria guianensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21322	Plinia cauliflora	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO816	Stenomesson miniatum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6469	Clematis angustifolia	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3619	Ilex hainanensis	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5868	Morus rubra	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4676	Melicope sarcococca	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5258	Fagara zanthoxyloides	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO12378	Streptomyces blastmyceticus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO11357	Nephelium lappaceum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3084	Xylopia brasiliensis	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4307	Canarium album	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10396	Pteris australis	Species	Pteridaceae	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 NPC307248 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	255
0.1-0.2	1683
0.2-0.3	5021
0.3-0.4	12217
0.4-0.5	10213
0.5-0.6	5958
0.6-0.7	4152
0.7-0.8	1948
0.8-0.85	649
0.85-0.9	243
0.9-0.95	133
0.95-1	225

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 NPC307248 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	234
0.1-0.2	1978
0.2-0.3	3878
0.3-0.4	2013
0.4-0.5	594
0.5-0.6	273
0.6-0.7	146
0.7-0.8	26
0.8-0.85	5
0.85-0.9	3
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