NPASS Compound

Structure

NPC101888 OpenBabel06302215112D 45 49 0 0 1 0 0 0 0 0999 V2000 -2.5981 2.5000 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 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 O 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 -1.7321 0.0000 0.0000 O 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 3 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.1340 -1.0647 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6337 -1.4402 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2507 -1.5405 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3312 -2.5373 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8436 -1.3426 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.0175 -1.9430 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6244 -2.0926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0575 -1.6418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8835 -1.0414 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2766 -0.8918 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4505 -0.2914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0434 -0.4893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5113 -0.0748 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3863 0.5377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7934 0.7356 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3255 0.3211 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.9302 0.8053 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5309 1.6047 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3551 1.0503 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1348 1.2008 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4599 -0.3915 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2435 -1.4691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5763 -0.3202 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0284 -1.8811 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9027 -3.0531 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 0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 10 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 9 1 0 0 0 0 5 6 1 0 0 0 0 5 8 1 0 0 0 0 6 7 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 43 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 45 1 0 0 0 0 15 36 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 44 1 0 0 0 0 17 18 1 0 0 0 0 17 43 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 22 27 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 42 1 0 0 0 0 25 26 1 0 0 0 0 25 41 1 0 0 0 0 26 27 2 0 0 0 0 26 40 1 0 0 0 0 27 28 1 0 0 0 0 28 33 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 29 39 1 0 0 0 0 30 31 2 0 0 0 0 30 38 1 0 0 0 0 31 32 1 0 0 0 0 31 37 1 0 0 0 0 32 33 1 0 0 0 0 33 34 1 0 0 0 0 34 35 2 0 0 0 0 34 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	638.11
Volume:	564.625
LogP:	-0.935
LogD:	0.094
LogS:	-2.15
# Rotatable Bonds:	3
TPSA:	310.66
# H-Bond Aceptor:	18
# H-Bond Donor:	11
# Rings:	5
# Heavy Atoms:	18

MedChem Properties

QED Drug-Likeness Score:	0.13
Synthetic Accessibility Score:	6.463
Fsp3:	0.37
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.731
MDCK Permeability:	2.356822369620204e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.97
Human Intestinal Absorption (HIA):	0.873
20% Bioavailability (F20%):	0.966
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.079
Plasma Protein Binding (PPB):	85.01819610595703%
Volume Distribution (VD):	0.523
Pgp-substrate:	15.413455963134766%

ADMET: Metabolism

CYP1A2-inhibitor:	0.013
CYP1A2-substrate:	0.008
CYP2C19-inhibitor:	0.017
CYP2C19-substrate:	0.036
CYP2C9-inhibitor:	0.015
CYP2C9-substrate:	0.051
CYP2D6-inhibitor:	0.0
CYP2D6-substrate:	0.097
CYP3A4-inhibitor:	0.029
CYP3A4-substrate:	0.004

ADMET: Excretion

Clearance (CL):	2.267
Half-life (T1/2):	0.948

ADMET: Toxicity

hERG Blockers:	0.003
Human Hepatotoxicity (H-HT):	0.076
Drug-inuced Liver Injury (DILI):	0.98
AMES Toxicity:	0.27
Rat Oral Acute Toxicity:	0.002
Maximum Recommended Daily Dose:	0.005
Skin Sensitization:	0.737
Carcinogencity:	0.029
Eye Corrosion:	0.003
Eye Irritation:	0.132
Respiratory Toxicity:	0.021

Download Data

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

Natural Product: NPC101888

Natural Product ID:	NPC101888
*Common Name:**	GCYIQTOCHJBSMY-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GCYIQTOCHJBSMY-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C27H26O18/c28-9-1-6(2-10(29)16(9)32)24(39)45-27-22(38)23-19(35)13(43-27)5-42-25(40)7-3-11(30)17(33)20(36)14(7)15-8(26(41)44-23)4-12(31)18(34)21(15)37/h1-2,7-8,13,19,22-23,27-38H,3-5H2
SMILES:	c1c(cc(c(c1O)O)O)C(=O)OC1C(C2C(C(COC(=O)C3CC(=C(C(=C3C3=C(C(=C(CC3C(=O)O2)O)O)O)O)O)O)O1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000238] Tannins [CHEMONTID:0001710] Hydrolyzable tannins

*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
NPO26650	Terminalia chebula	Species	Combretaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11520216]
NPO28450	Phyllanthus emblica	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11754604]
NPO30634	Acer nikoense	Species	Sapindaceae	Eukaryota	n.a.	Japan	n.a.	PMID[12542351]
NPO27007	Cunonia macrophylla	Species	Cunoniaceae	Eukaryota	n.a.	New Caledonia	n.a.	PMID[15652581]
NPO140	Coriaria japonica	Species	Coriariaceae	Eukaryota	n.a.	fruit	n.a.	PMID[16079545]
NPO28450	Phyllanthus emblica	Species	Phyllanthaceae	Eukaryota	Roots	Simao city, Yunnan Province, China	2007-MAY	PMID[19374435]
NPO30634	Acer nikoense	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21550801]
NPO25140	Sapium sebiferum	Species	Euphorbiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[26281591]
NPO24560	Ricinus communis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26509914]
NPO25140	Sapium sebiferum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3404159]
NPO31224	Sapium sebiferum	Species	Euphorbiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[7513748]
NPO21020	Phyllanthus urinaria	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO28450	Phyllanthus emblica	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21020	Phyllanthus urinaria	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11632	Fructus phyllanthi	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO31224	Sapium sebiferum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30634	Acer nikoense	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO140	Coriaria japonica	Species	Coriariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24560	Ricinus communis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27007	Cunonia macrophylla	Species	Cunoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5731	Euphorbia humifusa	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26650	Terminalia chebula	Species	Combretaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28169	Aleurites cordata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28169	Aleurites cordata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24560	Ricinus communis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27007	Cunonia macrophylla	Species	Cunoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO140	Coriaria japonica	Species	Coriariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13983	Acer maximowiczianum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28450	Phyllanthus emblica	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18030	Herba acalyphae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO11632	Fructus phyllanthi	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO26650	Terminalia chebula	Species	Combretaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO60	Neoshirakia japonica	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25140	Sapium sebiferum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21020	Phyllanthus urinaria	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5731	Euphorbia humifusa	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26650	Terminalia chebula	Species	Combretaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO140	Coriaria japonica	Species	Coriariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO31224	Sapium sebiferum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24560	Ricinus communis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28450	Phyllanthus emblica	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28169	Aleurites cordata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21020	Phyllanthus urinaria	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28450	Phyllanthus emblica	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26650	Terminalia chebula	Species	Combretaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO5731	Euphorbia humifusa	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO24560	Ricinus communis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27007	Cunonia macrophylla	Species	Cunoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO60	Neoshirakia japonica	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24560	Ricinus communis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26650	Terminalia chebula	Species	Combretaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25140	Sapium sebiferum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13983	Acer maximowiczianum	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO140	Coriaria japonica	Species	Coriariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5731	Euphorbia humifusa	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28450	Phyllanthus emblica	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21020	Phyllanthus urinaria	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28169	Aleurites cordata	Species	Euphorbiaceae	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 NPC101888 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	364
0.1-0.2	1420
0.2-0.3	3256
0.3-0.4	7091
0.4-0.5	10100
0.5-0.6	6159
0.6-0.7	7145
0.7-0.8	6322
0.8-0.85	696
0.85-0.9	114
0.9-0.95	30
0.95-1	0

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 NPC101888 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	314
0.1-0.2	880
0.2-0.3	1891
0.3-0.4	2711
0.4-0.5	1944
0.5-0.6	1013
0.6-0.7	298
0.7-0.8	92
0.8-0.85	7
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