NPASS Compound

Structure

NPC478951 OpenBabel06302215562D 51 54 0 0 1 0 0 0 0 0999 V2000 5.4247 2.9591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6735 2.3287 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8438 1.3631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8438 2.0338 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.4127 2.5477 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.7521 2.6641 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4167 1.7427 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7521 3.3349 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.1712 3.6703 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5903 3.3349 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5903 2.6641 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6097 2.6641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1194 1.8149 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1712 2.3287 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.9418 1.6984 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.1712 1.0681 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0009 2.0338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7521 2.6641 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4115 4.5955 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4901 4.9309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7389 4.3006 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3198 5.8966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0926 0.7327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7573 -0.1887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7230 -0.0184 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9612 1.6984 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4709 0.8492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9612 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4903 0.8492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.6984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9806 1.6984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4709 0.8492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9806 -0.0000 0.0000 C 0 0 0 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 2.1000 1.8149 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7411 3.8252 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8919 3.3349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8919 2.3543 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0426 3.8252 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6013 3.8252 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6013 4.8058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7521 5.2961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4505 5.2961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9030 3.3969 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8836 3.3969 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3738 2.5477 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3738 4.2461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7653 2.3692 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5165 1.7389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3462 0.7732 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4379 2.0743 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 18 1 0 0 0 0 2 3 2 0 0 0 0 3 23 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 4 48 1 0 0 0 0 5 6 1 0 0 0 0 5 44 1 0 0 0 0 6 14 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 40 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 36 1 0 0 0 0 11 12 1 0 0 0 0 11 14 1 0 0 0 0 11 35 1 0 0 0 0 12 13 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 26 1 0 0 0 0 16 17 1 0 0 0 0 16 23 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 20 21 2 0 0 0 0 20 22 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 29 34 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 31 32 1 0 0 0 0 32 33 2 0 0 0 0 33 34 1 0 0 0 0 36 37 1 0 0 0 0 37 38 2 0 0 0 0 37 39 1 0 0 0 0 40 41 1 0 0 0 0 41 42 2 0 0 0 0 41 43 1 0 0 0 0 44 45 1 0 0 0 0 45 46 2 0 0 0 0 45 47 1 0 0 0 0 48 49 1 0 0 0 0 49 50 2 0 0 0 0 49 51 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	716.3
Volume:	710.981
LogP:	3.686
LogD:	2.041
LogS:	-4.404
# Rotatable Bonds:	14
TPSA:	198.26
# H-Bond Aceptor:	14
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.226
Synthetic Accessibility Score:	5.875
Fsp3:	0.622
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:	-5.269
MDCK Permeability:	0.00019738441915251315
Pgp-inhibitor:	1.0
Pgp-substrate:	0.995
Human Intestinal Absorption (HIA):	0.654
20% Bioavailability (F20%):	0.329
30% Bioavailability (F30%):	0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.053
Plasma Protein Binding (PPB):	75.99970245361328%
Volume Distribution (VD):	1.929
Pgp-substrate:	13.648061752319336%

ADMET: Metabolism

CYP1A2-inhibitor:	0.019
CYP1A2-substrate:	0.008
CYP2C19-inhibitor:	0.008
CYP2C19-substrate:	0.058
CYP2C9-inhibitor:	0.053
CYP2C9-substrate:	0.023
CYP2D6-inhibitor:	0.455
CYP2D6-substrate:	0.041
CYP3A4-inhibitor:	0.338
CYP3A4-substrate:	0.329

ADMET: Excretion

Clearance (CL):	3.236
Half-life (T1/2):	0.334

ADMET: Toxicity

hERG Blockers:	0.051
Human Hepatotoxicity (H-HT):	0.976
Drug-inuced Liver Injury (DILI):	0.956
AMES Toxicity:	0.02
Rat Oral Acute Toxicity:	0.045
Maximum Recommended Daily Dose:	0.372
Skin Sensitization:	0.111
Carcinogencity:	0.019
Eye Corrosion:	0.003
Eye Irritation:	0.021
Respiratory Toxicity:	0.744

Download Data

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

Natural Product: NPC478951

Natural Product ID:	NPC478951
*Common Name:**	TXRVJIRDFOBPGO-YIFMMSFHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	TXRVJIRDFOBPGO-YIFMMSFHSA-N
Standard InCHI:	InChI=1S/C37H48O14/c1-18-26(46-19(2)39)15-25-30(51-34(44)24-13-11-10-12-14-24)32-36(9,27(47-20(3)40)16-28(48-21(4)41)37(32,45)17-38)33(50-23(6)43)31(49-22(5)42)29(18)35(25,7)8/h10-14,25-28,30-33,38,45H,15-17H2,1-9H3/t25-,26-,27-,28-,30+,31+,32-,33-,36+,37-/m0/s1
SMILES:	CC1=C2[C@H]([C@@H]([C@]3(C)[C@H](C[C@@H]([C@@](CO)([C@H]3[C@@H]([C@H](C[C@@H]1OC(=O)C)C2(C)C)OC(=O)c1ccccc1)O)OC(=O)C)OC(=O)C)OC(=O)C)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44584243
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0000676] Taxanes and derivatives

*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
NPO27746	Taxus mairei	Species	Taxaceae	Eukaryota	stem bark	n.a.	n.a.	PMID[11473432]
NPO27746	Taxus mairei	Species	Taxaceae	Eukaryota	Roots	n.a.	n.a.	PMID[8991951]
NPO27746	Taxus mairei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9644081]
NPO27746	Taxus mairei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27746	Taxus mairei	Species	Taxaceae	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

Activity Type	# Activity
IC50	4

Activity Type	# Activity
Cell Line	3
NON-MOLECULAR	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT168	Cell Line	P388	Mus musculus	IC50	=	2.4	ug.mL-1	PMID[8991951]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	4.8	ug.mL-1	PMID[8991951]
NPT139	Cell Line	HT-29	Homo sapiens	IC50	=	1.4	ug.mL-1	PMID[8991951]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	1.0	ug.mL-1	PMID[8991951]

☑ 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 NPC478951 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	300
0.1-0.2	1048
0.2-0.3	2302
0.3-0.4	4854
0.4-0.5	9174
0.5-0.6	11042
0.6-0.7	11847
0.7-0.8	1766
0.8-0.85	170
0.85-0.9	160
0.9-0.95	31
0.95-1	3

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 NPC478951 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	250
0.1-0.2	745
0.2-0.3	1513
0.3-0.4	2791
0.4-0.5	2168
0.5-0.6	1268
0.6-0.7	387
0.7-0.8	26
0.8-0.85	2
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