NPASS Compound

Structure

NPC110855 OpenBabel06302216192D 44 47 0 0 1 0 0 0 0 0999 V2000 -1.7333 -2.9470 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7333 -2.9470 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2333 -2.0810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7333 -1.2150 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2333 -0.3490 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7667 -0.3490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2667 0.5171 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0182 0.3455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2455 -0.3910 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2204 -0.6136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9006 0.1195 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6058 1.0751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6309 1.2976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2860 1.8081 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7212 -0.9561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4542 -1.6363 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4986 -1.9310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9696 -0.7846 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7424 -0.0480 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0262 0.0096 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5262 -0.8564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0262 -1.7224 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5262 -0.8564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0262 0.0096 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0262 0.0096 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5262 -0.8564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0262 -1.7224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0262 -1.7224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5262 -2.5885 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5262 -0.8564 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4605 0.6465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4493 0.4975 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2333 1.3831 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4011 2.3689 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3688 3.0072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2010 3.9930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7367 4.3406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9708 4.6312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7667 1.3831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2667 2.2491 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7333 0.5171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5993 0.0171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5993 1.0171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2333 -3.8131 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 44 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 41 1 0 0 0 0 7 6 1 1 0 0 0 7 19 1 0 0 0 0 7 39 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 1 0 0 0 9 15 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 12 14 1 0 0 0 0 15 16 1 0 0 0 0 15 17 1 0 0 0 0 15 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 20 31 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 23 28 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 26 30 1 0 0 0 0 27 28 1 0 0 0 0 27 29 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 33 34 1 6 0 0 0 33 39 1 0 0 0 0 33 41 1 0 0 0 0 34 35 1 0 0 0 0 35 36 2 0 0 0 0 36 37 1 0 0 0 0 36 38 1 0 0 0 0 39 40 2 0 0 0 0 41 42 1 0 0 0 0 41 43 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	602.36
Volume:	657.955
LogP:	8.615
LogD:	5.561
LogS:	-4.17
# Rotatable Bonds:	8
TPSA:	100.9
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.102
Synthetic Accessibility Score:	6.122
Fsp3:	0.553
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	2
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.023
MDCK Permeability:	1.2797279850929044e-05
Pgp-inhibitor:	0.138
Pgp-substrate:	0.188
Human Intestinal Absorption (HIA):	0.144
20% Bioavailability (F20%):	0.995
30% Bioavailability (F30%):	0.971

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.013
Plasma Protein Binding (PPB):	100.4446792602539%
Volume Distribution (VD):	1.122
Pgp-substrate:	7.809916973114014%

ADMET: Metabolism

CYP1A2-inhibitor:	0.088
CYP1A2-substrate:	0.143
CYP2C19-inhibitor:	0.837
CYP2C19-substrate:	0.173
CYP2C9-inhibitor:	0.913
CYP2C9-substrate:	0.911
CYP2D6-inhibitor:	0.91
CYP2D6-substrate:	0.031
CYP3A4-inhibitor:	0.834
CYP3A4-substrate:	0.781

ADMET: Excretion

Clearance (CL):	15.188
Half-life (T1/2):	0.059

ADMET: Toxicity

hERG Blockers:	0.013
Human Hepatotoxicity (H-HT):	0.973
Drug-inuced Liver Injury (DILI):	0.943
AMES Toxicity:	0.023
Rat Oral Acute Toxicity:	0.607
Maximum Recommended Daily Dose:	0.825
Skin Sensitization:	0.167
Carcinogencity:	0.304
Eye Corrosion:	0.003
Eye Irritation:	0.057
Respiratory Toxicity:	0.94

Download Data

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

Natural Product: NPC110855

Natural Product ID:	NPC110855
*Common Name:**	KXTNVBQRLRYVCO-OGHRFRAUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KXTNVBQRLRYVCO-OGHRFRAUSA-N
Standard InCHI:	InChI=1S/C38H50O6/c1-22(2)11-14-26-20-37-21-27(15-12-23(3)4)36(9,10)44-33(37)30(31(41)25-13-16-28(39)29(40)19-25)32(42)38(34(37)43,35(26,7)8)18-17-24(5)6/h11-13,16-17,19,26-27,39-40H,14-15,18,20-21H2,1-10H3/t26-,27-,37-,38-/m1/s1
SMILES:	CC(=CC[C@@H]1C[C@@]23C[C@@H](CC=C(C)C)C(C)(C)OC2=C(C(=O)c2ccc(c(c2)O)O)C(=O)[C@](CC=C(C)C)(C3=O)C1(C)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	21125413
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001549] Monoterpenoids [CHEMONTID:0000051] Aromatic monoterpenoids

*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
NPO5638	Garcinia livingstonei	Species	Clusiaceae	Eukaryota	n.a.	fruit	n.a.	DOI[10.1016/S0040-4020(01)89039-6]
NPO5638	Garcinia livingstonei	Species	Clusiaceae	Eukaryota	root bark	n.a.	n.a.	PMID[16562837]
NPO30436	Rheedia edulis	Species	Clusiaceae	Eukaryota	n.a.	seed	n.a.	PMID[21028890]
NPO5638	Garcinia livingstonei	Species	Clusiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[21028890]
NPO30436	Rheedia edulis	Species	Clusiaceae	Eukaryota	n.a.	exocarp	n.a.	PMID[21028890]
NPO30436	Rheedia edulis	Species	Clusiaceae	Eukaryota	seeds and rinds	n.a.	n.a.	PMID[21028890]
NPO40852	Garcinia picrorhiza	Species	Clusiaceae	Eukaryota	Stem Bark	n.a.	n.a.	PMID[32627543]
NPO3858	Pimpinella magna	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4768	Lunaria annua	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3858	Pimpinella magna	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10493	Casearia thwaitesii	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1970	Rubus palmatus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6556	Garcinia intermedia	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5638	Garcinia livingstonei	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO104	Hymenodictyon floribundum	Species	Rubiaceae	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	5
Others	1

Activity Type	# Activity
Cell Line	5
CELL-LINE	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT113	Cell Line	RAW264.7	Mus musculus	Inhibition	=	92.94	%	PMID[31255927]
NPT139	Cell Line	HT-29	Homo sapiens	IC50	>	10000.0	nM	PMID[32627543]
NPT91	Cell Line	KB	Homo sapiens	IC50	=	5300.0	nM	PMID[32627543]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	7200.0	nM	PMID[32627543]
NPT65	Cell Line	HepG2	Homo sapiens	IC50	>	10000.0	nM	PMID[32627543]
NPT20987	CELL-LINE	HeLa S3	Homo sapiens	IC50	>	10000.0	nM	PMID[32627543]

☑ 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 NPC110855 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	393
0.1-0.2	1480
0.2-0.3	2866
0.3-0.4	7332
0.4-0.5	11091
0.5-0.6	6963
0.6-0.7	10113
0.7-0.8	2363
0.8-0.85	33
0.85-0.9	14
0.9-0.95	40
0.95-1	9

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 NPC110855 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	348
0.1-0.2	904
0.2-0.3	1438
0.3-0.4	2794
0.4-0.5	2230
0.5-0.6	1032
0.6-0.7	385
0.7-0.8	18
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