NPASS Compound

Structure

NPC41943 OpenBabel06302216172D 57 61 0 0 1 0 0 0 0 0999 V2000 8.2084 15.9369 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0640 15.4434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0645 14.4557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2093 13.9615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2097 12.9738 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3545 12.4796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3550 11.4919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4998 10.9976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5002 10.0099 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6450 9.5157 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6455 8.5280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7903 8.0338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7907 7.0461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9356 6.5519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9360 5.5641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0808 5.0699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2252 5.5634 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0812 4.0822 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4206 3.3479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7263 2.4087 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6925 2.2037 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.9981 1.2645 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3375 0.5302 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.3713 0.7351 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7107 0.0009 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8551 0.4943 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8548 1.4825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0006 1.9764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8557 1.4821 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8560 2.4843 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8554 0.4939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7111 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5671 0.4934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5673 1.4816 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4233 1.9754 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1338 1.9749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1341 2.9625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2796 3.4569 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2799 4.4441 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.2981 4.5475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8604 5.2426 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4591 6.1445 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0396 6.9430 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.6383 7.8450 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0213 6.8395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6018 7.6380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4226 5.9376 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4236 2.9630 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4239 3.9630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5679 3.4574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7119 2.9635 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7116 1.9759 0.0000 C 0 0 2 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 2.0657 1.6744 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6431 -0.4090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9643 1.0596 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3531 2.9380 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 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 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 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 20 19 1 6 0 0 0 20 21 1 0 0 0 0 20 54 1 0 0 0 0 21 22 1 0 0 0 0 21 57 1 1 0 0 0 22 23 1 0 0 0 0 22 56 1 6 0 0 0 23 24 1 0 0 0 0 23 55 1 1 0 0 0 24 25 1 6 0 0 0 24 54 1 0 0 0 0 26 25 1 6 0 0 0 26 27 1 0 0 0 0 26 53 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 52 1 0 0 0 0 29 30 1 6 0 0 0 29 31 1 0 0 0 0 31 32 2 0 0 0 0 31 53 1 0 0 0 0 32 33 1 0 0 0 0 34 33 1 1 0 0 0 34 35 1 0 0 0 0 34 52 1 0 0 0 0 35 36 1 6 0 0 0 35 48 1 0 0 0 0 36 37 1 0 0 0 0 37 38 1 0 0 0 0 38 39 1 6 0 0 0 38 48 1 0 0 0 0 39 40 1 1 0 0 0 39 41 1 0 0 0 0 41 42 1 0 0 0 0 42 43 1 0 0 0 0 43 44 1 1 0 0 0 43 45 1 0 0 0 0 45 46 1 0 0 0 0 45 47 1 0 0 0 0 48 49 1 6 0 0 0 48 50 1 0 0 0 0 50 51 1 0 0 0 0 52 51 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	324.14
Volume:	342.876
LogP:	5.191
LogD:	3.682
LogS:	-3.61
# Rotatable Bonds:	3
TPSA:	66.76
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.826
Synthetic Accessibility Score:	3.09
Fsp3:	0.25
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.696
MDCK Permeability:	1.7832064258982427e-05
Pgp-inhibitor:	0.091
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.533
30% Bioavailability (F30%):	0.265

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.079
Plasma Protein Binding (PPB):	98.80037689208984%
Volume Distribution (VD):	0.847
Pgp-substrate:	1.6645680665969849%

ADMET: Metabolism

CYP1A2-inhibitor:	0.839
CYP1A2-substrate:	0.343
CYP2C19-inhibitor:	0.956
CYP2C19-substrate:	0.104
CYP2C9-inhibitor:	0.924
CYP2C9-substrate:	0.94
CYP2D6-inhibitor:	0.881
CYP2D6-substrate:	0.448
CYP3A4-inhibitor:	0.51
CYP3A4-substrate:	0.166

ADMET: Excretion

Clearance (CL):	12.971
Half-life (T1/2):	0.167

ADMET: Toxicity

hERG Blockers:	0.057
Human Hepatotoxicity (H-HT):	0.797
Drug-inuced Liver Injury (DILI):	0.857
AMES Toxicity:	0.158
Rat Oral Acute Toxicity:	0.846
Maximum Recommended Daily Dose:	0.853
Skin Sensitization:	0.854
Carcinogencity:	0.264
Eye Corrosion:	0.003
Eye Irritation:	0.838
Respiratory Toxicity:	0.858

Download Data

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

Natural Product: NPC41943

Natural Product ID:	NPC41943
*Common Name:**	DAPLORBFRRJHHY-ODZGBWFKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DAPLORBFRRJHHY-ODZGBWFKSA-N
Standard InCHI:	InChI=1S/C50H88O7/c1-8-9-10-11-12-13-14-15-16-17-18-19-20-21-44(51)55-33-43-45(52)46(53)47(54)48(57-43)56-38-28-30-49(6)37(32-38)24-25-39-41-27-26-40(50(41,7)31-29-42(39)49)36(5)23-22-35(4)34(2)3/h24,34-36,38-43,45-48,52-54H,8-23,25-33H2,1-7H3/t35-,36+,38-,39-,40+,41-,42-,43+,45+,46-,47+,48+,49-,50+/m0/s1
SMILES:	CCCCCCCCCCCCCCCC(=O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@H](O[C@H]2CC[C@@]3(C)C(=CC[C@H]4[C@@H]5CC[C@H]([C@H](C)CC[C@H](C)C(C)C)[C@@]5(C)CC[C@H]34)C2)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	13051627
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001013] Steroidal glycosides

*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
NPO12525	Eriosema chinense	Species	Fabaceae	Eukaryota	Roots	n.a.	n.a.	PMID[19555123]
NPO26763	Rhododendron micranthum	Species	Ericaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[30452260]
NPO7049	Trichocolea tomentella	Species	Trichocoleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8792619]
NPO26763	Rhododendron micranthum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8133	Woodwardia orientalis	Species	Blechnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26763	Rhododendron micranthum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8133	Woodwardia orientalis	Species	Blechnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8133	Woodwardia orientalis	Species	Blechnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26763	Rhododendron micranthum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5287	Strychnos cathayensis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7049	Trichocolea tomentella	Species	Trichocoleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12525	Eriosema chinense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26763	Rhododendron micranthum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8133	Woodwardia orientalis	Species	Blechnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9572	Myrtopsis sellingii	Species	Rutaceae	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 NPC41943 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	217
0.1-0.2	1327
0.2-0.3	4594
0.3-0.4	11145
0.4-0.5	9971
0.5-0.6	5837
0.6-0.7	5144
0.7-0.8	3549
0.8-0.85	703
0.85-0.9	161
0.9-0.95	44
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 NPC41943 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	186
0.1-0.2	1581
0.2-0.3	3904
0.3-0.4	2279
0.4-0.5	644
0.5-0.6	233
0.6-0.7	216
0.7-0.8	100
0.8-0.85	6
0.85-0.9	1
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