NPASS Compound

Structure

NPC92598 OpenBabel06302215172D 47 53 0 0 1 0 0 0 0 0999 V2000 5.1412 -2.1468 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7085 -2.9509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7958 -2.9783 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3158 -2.2016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4031 -2.2290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9230 -1.4522 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0103 -1.4796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5303 -0.7029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3824 -0.7303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1785 -0.2831 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.8253 -0.9490 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7523 -0.9490 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6408 -0.0941 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8287 0.0976 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3298 0.7665 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3542 2.6665 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3479 2.8453 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3776 1.5995 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9497 2.2069 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7784 2.3045 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9417 3.1228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2139 3.5310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0958 4.5337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6008 2.9649 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3894 3.1625 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8253 1.2959 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.7523 1.2959 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.1254 2.1784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3992 0.6300 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3992 -0.2831 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1492 -0.8038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5261 -1.6355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6811 -0.0616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2889 0.4877 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2453 0.9733 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0275 0.5022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0106 -0.4107 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8265 0.9441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8434 1.8570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6425 2.2989 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4247 1.8278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4078 0.9148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6087 0.4730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1785 0.6300 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3017 1.2606 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5498 1.9986 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 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 7 8 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 34 1 0 0 0 0 10 44 1 0 0 0 0 10 11 1 0 0 0 0 12 11 1 1 0 0 0 12 13 1 0 0 0 0 12 30 1 0 0 0 0 13 14 1 0 0 0 0 13 26 1 0 0 0 0 14 15 1 0 0 0 0 14 47 1 1 0 0 0 15 16 1 0 0 0 0 15 18 1 0 0 0 0 15 47 1 0 0 0 0 16 17 1 0 0 0 0 18 19 1 0 0 0 0 18 46 1 6 0 0 0 19 24 1 0 0 0 0 19 20 1 0 0 0 0 19 45 1 0 0 0 0 20 21 1 6 0 0 0 20 26 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 22 24 1 0 0 0 0 24 25 2 0 0 0 0 26 27 1 0 0 0 0 26 44 1 0 0 0 0 27 28 1 0 0 0 0 27 29 1 0 0 0 0 29 30 1 0 0 0 0 29 35 1 0 0 0 0 30 31 1 0 0 0 0 30 34 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 35 36 1 0 0 0 0 36 37 2 0 0 0 0 36 38 1 0 0 0 0 38 43 2 0 0 0 0 38 39 1 0 0 0 0 39 40 2 0 0 0 0 40 41 1 0 0 0 0 41 42 2 0 0 0 0 42 43 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	648.29
Volume:	652.787
LogP:	4.663
LogD:	3.264
LogS:	-3.674
# Rotatable Bonds:	11
TPSA:	144.28
# H-Bond Aceptor:	10
# H-Bond Donor:	3
# Rings:	7
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.113
Synthetic Accessibility Score:	6.696
Fsp3:	0.568
Lipinski Rule-of-5:	Accepted
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:	-4.921
MDCK Permeability:	1.3383325494942255e-05
Pgp-inhibitor:	0.915
Pgp-substrate:	0.014
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.098
30% Bioavailability (F30%):	0.811

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.507
Plasma Protein Binding (PPB):	91.51283264160156%
Volume Distribution (VD):	1.817
Pgp-substrate:	4.045528888702393%

ADMET: Metabolism

CYP1A2-inhibitor:	0.041
CYP1A2-substrate:	0.94
CYP2C19-inhibitor:	0.26
CYP2C19-substrate:	0.522
CYP2C9-inhibitor:	0.866
CYP2C9-substrate:	0.024
CYP2D6-inhibitor:	0.017
CYP2D6-substrate:	0.419
CYP3A4-inhibitor:	0.889
CYP3A4-substrate:	0.562

ADMET: Excretion

Clearance (CL):	5.898
Half-life (T1/2):	0.291

ADMET: Toxicity

hERG Blockers:	0.821
Human Hepatotoxicity (H-HT):	0.941
Drug-inuced Liver Injury (DILI):	0.939
AMES Toxicity:	0.16
Rat Oral Acute Toxicity:	0.307
Maximum Recommended Daily Dose:	0.97
Skin Sensitization:	0.677
Carcinogencity:	0.881
Eye Corrosion:	0.003
Eye Irritation:	0.014
Respiratory Toxicity:	0.986

Download Data

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

Natural Product: NPC92598

Natural Product ID:	NPC92598
*Common Name:**	CGSGRJNIABXQJQ-CAAOHEDASA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CGSGRJNIABXQJQ-CAAOHEDASA-N
Standard InCHI:	InChI=1S/C37H44O10/c1-6-7-8-9-10-11-15-18-34-45-30-26-29-33(20-38,44-29)32(41)35(42)25(19-22(4)27(35)39)37(26,47-34)23(5)28(36(30,46-34)21(2)3)43-31(40)24-16-13-12-14-17-24/h10-19,23,25-26,28-30,32,38,41-42H,2,6-9,20H2,1,3-5H3/b11-10+,18-15+/t23-,25-,26+,28-,29+,30-,32-,33+,34?,35-,36+,37+/m1/s1
SMILES:	CCCCC/C=C/C=C/C12O[C@@H]3[C@@H]4[C@H]5[C@@](CO)([C@H]([C@]6([C@@H](C=C(C)C6=O)[C@]4([C@H](C)[C@H]([C@]3(C(=C)C)O1)OC(=O)c1ccccc1)O2)O)O)O5
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	6440205
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0003494] Rhamnofolane and daphnane 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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32997496]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32223193]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31860304]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	Roots	n.a.	n.a.	PMID[31150241]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27228307]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	flower buds	n.a.	n.a.	PMID[23558238]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	flower	n.a.	PMID[21916433]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6789	Gnidia latifolia	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

Activity Type	# Activity
Others	2

Activity Type	# Activity
Organism	1
SINGLE PROTEIN	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Activity	=	40.28	%	PMID[27228307]
NPT17120	SINGLE PROTEIN	Nuclear receptor subfamily 4 group A member 2	Mus musculus	FC	=	3.5	n.a.	PMID[27228307]

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☑ 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 NPC92598 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	351
0.1-0.2	1208
0.2-0.3	2637
0.3-0.4	5280
0.4-0.5	10295
0.5-0.6	11347
0.6-0.7	9731
0.7-0.8	1461
0.8-0.85	296
0.85-0.9	54
0.9-0.95	18
0.95-1	19

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Similarity Score	Similarity Level	Natural Product ID
No data available in table

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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 NPC92598 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	286
0.1-0.2	789
0.2-0.3	1710
0.3-0.4	3026
0.4-0.5	2210
0.5-0.6	861
0.6-0.7	240
0.7-0.8	28
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
No data available in table

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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