NPASS Compound

Structure

NPC91879 OpenBabel06302215362D 34 37 0 0 1 0 0 0 0 0999 V2000 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 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 2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 21 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 3 34 1 0 0 0 0 4 18 1 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 1 0 0 0 8 17 1 0 0 0 0 9 14 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 15 1 0 0 0 0 13 14 1 0 0 0 0 15 16 1 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 23 22 1 1 0 0 0 23 24 1 0 0 0 0 23 30 1 0 0 0 0 24 25 1 0 0 0 0 24 33 1 6 0 0 0 25 26 1 0 0 0 0 25 32 1 1 0 0 0 26 27 1 0 0 0 0 26 31 1 6 0 0 0 27 28 1 1 0 0 0 27 30 1 0 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	476.17
Volume:	458.881
LogP:	2.29
LogD:	1.326
LogS:	-3.601
# Rotatable Bonds:	5
TPSA:	155.14
# H-Bond Aceptor:	10
# H-Bond Donor:	5
# Rings:	4
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.42
Synthetic Accessibility Score:	4.124
Fsp3:	0.458
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.824
MDCK Permeability:	1.4246493265090976e-05
Pgp-inhibitor:	0.081
Pgp-substrate:	0.938
Human Intestinal Absorption (HIA):	0.028
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.058

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.107
Plasma Protein Binding (PPB):	90.64529418945312%
Volume Distribution (VD):	0.928
Pgp-substrate:	6.753124237060547%

ADMET: Metabolism

CYP1A2-inhibitor:	0.031
CYP1A2-substrate:	0.196
CYP2C19-inhibitor:	0.04
CYP2C19-substrate:	0.738
CYP2C9-inhibitor:	0.041
CYP2C9-substrate:	0.619
CYP2D6-inhibitor:	0.146
CYP2D6-substrate:	0.311
CYP3A4-inhibitor:	0.078
CYP3A4-substrate:	0.193

ADMET: Excretion

Clearance (CL):	6.806
Half-life (T1/2):	0.215

ADMET: Toxicity

hERG Blockers:	0.106
Human Hepatotoxicity (H-HT):	0.363
Drug-inuced Liver Injury (DILI):	0.93
AMES Toxicity:	0.231
Rat Oral Acute Toxicity:	0.61
Maximum Recommended Daily Dose:	0.029
Skin Sensitization:	0.795
Carcinogencity:	0.292
Eye Corrosion:	0.003
Eye Irritation:	0.039
Respiratory Toxicity:	0.089

Download Data

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

Natural Product: NPC91879

Natural Product ID:	NPC91879
*Common Name:**	HPXOUFFMSLZOLE-WUQIJIJDSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HPXOUFFMSLZOLE-WUQIJIJDSA-N
Standard InCHI:	InChI=1S/C24H28O10/c1-10-18(27)17-14(26)8-15(12-4-6-13(31-3)7-5-12)32-23(17)11(2)22(10)34-24-21(30)20(29)19(28)16(9-25)33-24/h4-7,15-16,19-21,24-25,27-30H,8-9H2,1-3H3/t15-,16+,19+,20-,21+,24-/m0/s1
SMILES:	Cc1c(c2C(=O)C[C@@H](c3ccc(cc3)OC)Oc2c(C)c1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10457684
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003533] Flavonoid-7-O-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
NPO5638	Garcinia livingstonei	Species	Clusiaceae	Eukaryota	n.a.	fruit	n.a.	DOI[10.1016/S0040-4020(01)89039-6]
NPO4703	Solanum hispidum	Species	Solanaceae	Eukaryota	leaves	n.a.	n.a.	PMID[15217270]
NPO46	Onosma hispida	Species	Boraginaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[16079517]
NPO5638	Garcinia livingstonei	Species	Clusiaceae	Eukaryota	root bark	n.a.	n.a.	PMID[16562837]
NPO5638	Garcinia livingstonei	Species	Clusiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[21028890]
NPO14359	Pentarhizidium orientale	Species	Onocleaceae	Eukaryota	Rhizomes	n.a.	n.a.	PMID[28984452]
NPO46	Onosma hispida	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14359	Pentarhizidium orientale	Species	Onocleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO46	Onosma hispida	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2828	Blaps mucronata	Species	Tenebrionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3789	Lyonia formosa	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14359	Pentarhizidium orientale	Species	Onocleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5638	Garcinia livingstonei	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27945	Cancrinia discoidea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1896	Proteus penneri	Species	Morganellaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO46	Onosma hispida	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4703	Solanum hispidum	Species	Solanaceae	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 NPC91879 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	374
0.1-0.2	1502
0.2-0.3	3477
0.3-0.4	8720
0.4-0.5	9760
0.5-0.6	4273
0.6-0.7	5453
0.7-0.8	5688
0.8-0.85	2191
0.85-0.9	1066
0.9-0.95	168
0.95-1	25

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 NPC91879 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	324
0.1-0.2	869
0.2-0.3	1679
0.3-0.4	2670
0.4-0.5	1978
0.5-0.6	1077
0.6-0.7	357
0.7-0.8	152
0.8-0.85	32
0.85-0.9	12
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