NPASS Compound

Structure

NPC121973 OpenBabel06302216212D 33 39 0 0 1 0 0 0 0 0999 V2000 3.3766 1.9495 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3766 0.9747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2208 0.4874 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2208 -0.4874 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3766 -0.9747 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3766 -1.9495 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5325 -2.4369 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6883 -1.9495 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6883 -2.9242 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8442 -2.4369 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5325 -3.4116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8442 -3.4116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.8990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8442 -3.4116 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8442 -2.4369 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8442 -1.4621 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6883 -1.9495 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5325 -2.4369 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5325 -3.4116 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6883 -3.8990 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1757 -4.7431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2009 -4.7431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3766 -3.8990 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.9495 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -0.9747 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8442 -0.4874 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6883 -0.9747 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5325 -0.4874 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5325 0.4874 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1104 -0.2437 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9545 -0.2437 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4419 0.6005 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 2 0 0 0 0 2 29 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 28 1 0 0 0 0 5 31 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 27 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 10 24 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 20 1 0 0 0 0 15 16 1 0 0 0 0 15 17 1 0 0 0 0 15 24 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 23 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 25 33 1 0 0 0 0 26 27 1 0 0 0 0 26 33 1 0 0 0 0 27 28 1 0 0 0 0 27 30 1 0 0 0 0 28 29 1 6 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	456.29
Volume:	471.627
LogP:	3.766
LogD:	3.391
LogS:	-4.918
# Rotatable Bonds:	0
TPSA:	79.29
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	7
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.325
Synthetic Accessibility Score:	6.664
Fsp3:	0.893
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.233
MDCK Permeability:	2.2422802430810407e-05
Pgp-inhibitor:	0.003
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.082
30% Bioavailability (F30%):	0.443

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.88
Plasma Protein Binding (PPB):	74.38813781738281%
Volume Distribution (VD):	1.095
Pgp-substrate:	21.365543365478516%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.615
CYP2C19-inhibitor:	0.025
CYP2C19-substrate:	0.726
CYP2C9-inhibitor:	0.071
CYP2C9-substrate:	0.045
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.197
CYP3A4-inhibitor:	0.747
CYP3A4-substrate:	0.253

ADMET: Excretion

Clearance (CL):	5.218
Half-life (T1/2):	0.129

ADMET: Toxicity

hERG Blockers:	0.728
Human Hepatotoxicity (H-HT):	0.738
Drug-inuced Liver Injury (DILI):	0.027
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.97
Maximum Recommended Daily Dose:	0.923
Skin Sensitization:	0.191
Carcinogencity:	0.21
Eye Corrosion:	0.016
Eye Irritation:	0.025
Respiratory Toxicity:	0.984

Download Data

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

Natural Product: NPC121973

Natural Product ID:	NPC121973
*Common Name:**	SZILVBCYKIZRPO-MOBNGVPASA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SZILVBCYKIZRPO-MOBNGVPASA-N
Standard InCHI:	InChI=1S/C28H40O5/c1-15-6-11-27-13-12-25(4)24(3)10-7-16-23(2,9-8-18(29)26(16,5)31)20(24)19-21(32-19)28(25,17(27)14-15)33-22(27)30/h16-21,29,31H,1,6-14H2,2-5H3/t16-,17-,18+,19+,20-,21+,23+,24-,25+,26-,27+,28-/m1/s1
SMILES:	C=C1CC[C@]23CC[C@@]4(C)[C@]5(C)CC[C@@H]6[C@](C)(CC[C@@H]([C@]6(C)O)O)[C@H]5[C@H]5[C@@H]([C@@]4([C@@H]2C1)OC3=O)O5
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	56601458
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000050] Lactones [CHEMONTID:0001245] Gamma butyrolactones

*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
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	n.a.	root	n.a.	PMID[21954959]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	roots	Whitessence Srl, Viterbo, Italy	2005-OCT	PMID[21954959]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	n.a.	seed	n.a.	PMID[23497864]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	DingXi, GanSu, China	early autumn (from August to the beginning of September	PMID[32545196]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	LanZhou, GanSu, China	early autumn (from August to the beginning of September	PMID[32545196]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	90 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	30 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	Maturation	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	40 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	50 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	60 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	70 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	80 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	90 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	Maturation	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	10 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	20 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	30 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	40 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	50 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	60 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	10 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	70 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Seeds	Yangling, Shaanxi, China	80 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	Eukaryota	Fruits	Yangling, Shaanxi, China	20 days after pollination	PMID[33131958]
NPO15265	Paeonia rockii	Species	Paeoniaceae	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 NPC121973 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	272
0.1-0.2	2053
0.2-0.3	6207
0.3-0.4	12869
0.4-0.5	8840
0.5-0.6	5427
0.6-0.7	4348
0.7-0.8	2480
0.8-0.85	168
0.85-0.9	28
0.9-0.95	4
0.95-1	1

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 NPC121973 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	263
0.1-0.2	2391
0.2-0.3	3991
0.3-0.4	1628
0.4-0.5	466
0.5-0.6	250
0.6-0.7	138
0.7-0.8	22
0.8-0.85	1
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