NPASS Compound

Structure

NPC290753 OpenBabel06302215392D 54 59 0 0 1 0 0 0 0 0999 V2000 -2.2992 -8.2960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2992 -8.2960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7992 -7.4300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2992 -6.5639 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7992 -5.6979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2992 -4.8319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2992 -4.8319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7992 -3.9659 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.1953 -3.8613 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4032 -2.8832 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4628 -2.3832 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0561 -1.4696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2059 -3.0523 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1570 -2.7433 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.3649 -1.7651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6218 -1.0960 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8297 -0.1179 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5728 -0.7870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7807 0.1911 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9886 1.1693 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2455 1.8384 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2944 1.5294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9854 2.4805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3163 1.7373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0865 0.5513 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1355 0.2422 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0724 -0.7359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6707 -1.4050 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2804 -1.7141 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6077 0.9114 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3998 1.8895 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1429 2.5587 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9350 3.5368 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0161 3.8458 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7592 3.1767 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7103 3.4857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9182 4.4639 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5513 2.1985 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2240 4.8240 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6781 4.2059 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0940 2.2496 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8371 2.9188 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.7882 2.6097 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.5313 3.2789 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3234 4.2570 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3723 4.5660 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.1644 5.5442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6292 3.8969 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0665 4.9262 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4824 2.9699 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9961 1.6316 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4534 2.8166 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9001 -3.4124 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7992 -9.1620 0.0000 C 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 54 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 8 6 1 6 0 0 0 8 9 1 0 0 0 0 8 13 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 28 1 0 0 0 0 11 12 1 1 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 53 1 0 0 0 0 16 15 1 1 0 0 0 16 17 1 0 0 0 0 16 28 1 0 0 0 0 17 25 1 0 0 0 0 17 18 1 1 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 21 52 1 6 0 0 0 22 23 1 0 0 0 0 22 24 1 0 0 0 0 25 22 1 6 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 26 30 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 31 38 1 0 0 0 0 32 33 1 0 0 0 0 32 41 1 0 0 0 0 33 34 1 0 0 0 0 33 40 1 0 0 0 0 34 35 1 0 0 0 0 34 39 1 0 0 0 0 35 36 1 0 0 0 0 35 38 1 0 0 0 0 36 37 1 0 0 0 0 41 42 1 0 0 0 0 42 43 1 0 0 0 0 42 48 1 0 0 0 0 43 44 1 0 0 0 0 43 51 1 0 0 0 0 44 45 1 0 0 0 0 44 50 1 0 0 0 0 45 46 1 0 0 0 0 45 49 1 0 0 0 0 46 47 1 0 0 0 0 46 48 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	766.49
Volume:	783.859
LogP:	4.448
LogD:	3.641
LogS:	-4.42
# Rotatable Bonds:	9
TPSA:	198.76
# H-Bond Aceptor:	12
# H-Bond Donor:	8
# Rings:	6
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.126
Synthetic Accessibility Score:	5.955
Fsp3:	0.905
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:	-5.521
MDCK Permeability:	2.944262269011233e-05
Pgp-inhibitor:	0.998
Pgp-substrate:	0.972
Human Intestinal Absorption (HIA):	0.882
20% Bioavailability (F20%):	0.054
30% Bioavailability (F30%):	0.232

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.065
Plasma Protein Binding (PPB):	78.41142272949219%
Volume Distribution (VD):	0.514
Pgp-substrate:	11.334871292114258%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.107
CYP2C19-inhibitor:	0.002
CYP2C19-substrate:	0.581
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.032
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.056
CYP3A4-inhibitor:	0.117
CYP3A4-substrate:	0.058

ADMET: Excretion

Clearance (CL):	0.931
Half-life (T1/2):	0.414

ADMET: Toxicity

hERG Blockers:	0.492
Human Hepatotoxicity (H-HT):	0.242
Drug-inuced Liver Injury (DILI):	0.018
AMES Toxicity:	0.063
Rat Oral Acute Toxicity:	0.743
Maximum Recommended Daily Dose:	0.119
Skin Sensitization:	0.633
Carcinogencity:	0.091
Eye Corrosion:	0.003
Eye Irritation:	0.008
Respiratory Toxicity:	0.983

Download Data

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

Natural Product: NPC290753

Natural Product ID:	NPC290753
*Common Name:**	ZVTVWDXRNMHGNY-VEMRYNFXSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZVTVWDXRNMHGNY-VEMRYNFXSA-N
Standard InCHI:	InChI=1S/C42H70O12/c1-20(2)11-10-12-21(3)23-13-16-41(8)29(23)24(44)17-27-40(7)15-14-28(45)39(5,6)36(40)25(18-42(27,41)9)52-38-35(33(49)31(47)26(19-43)53-38)54-37-34(50)32(48)30(46)22(4)51-37/h11,22-38,43-50H,3,10,12-19H2,1-2,4-9H3/t22-,23+,24-,25+,26-,27-,28-,29+,30-,31-,32+,33+,34-,35-,36-,37+,38-,40-,41+,42-/m0/s1
SMILES:	CC(=CCCC(=C)[C@H]1CC[C@]2(C)[C@H]1[C@H](C[C@H]1[C@]3(C)CC[C@@H](C(C)(C)[C@@H]3[C@@H](C[C@]21C)O[C@@H]1[C@H]([C@@H]([C@H]([C@H](CO)O1)O)O)O[C@@H]1[C@H]([C@@H]([C@H]([C@H](C)O1)O)O)O)O)O)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: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
NPO210	Uvaria calamistrata	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10075755]
NPO210	Uvaria calamistrata	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11000019]
NPO11248	Tachigalia paniculata	n.a.	n.a.	n.a.	leaves	n.a.	n.a.	PMID[12444671]
NPO10540	Passiflora incarnata	Species	Passifloraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2026709]
NPO10540	Passiflora incarnata	Species	Passifloraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10540	Passiflora incarnata	Species	Passifloraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14255	Streptomyces flocculus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO19635	Coreopsis nodosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7998	Senecio paludaffinis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22666	Haematococcus lacustris	Species	Haematococcaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13166	Nicotiana undulata	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO731	Panax schinseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11488	Alstonia muelleriana	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14354	Artemisia cina	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10540	Passiflora incarnata	Species	Passifloraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11248	Tachigalia paniculata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO11642	Dacrydium cupressinum	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5189	Glycine tomentella	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12684	Trigonella grandiflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12001	Saccharomyces pastori	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13568	Hypoxylon rubiginosum	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21854	Pterocladiella tenuis	Species	Gelidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18805	Tripolium pannonicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO210	Uvaria calamistrata	Species	Annonaceae	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 NPC290753 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	254
0.1-0.2	1993
0.2-0.3	6464
0.3-0.4	13696
0.4-0.5	8950
0.5-0.6	5146
0.6-0.7	3384
0.7-0.8	1560
0.8-0.85	744
0.85-0.9	299
0.9-0.95	148
0.95-1	59

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 NPC290753 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	206
0.1-0.2	2172
0.2-0.3	4307
0.3-0.4	1629
0.4-0.5	447
0.5-0.6	235
0.6-0.7	125
0.7-0.8	16
0.8-0.85	5
0.85-0.9	8
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