NPASS Compound

Structure

CID127235 OpenBabel06191715482D 27 29 0 0 1 0 0 0 0 0999 V2000 1.8074 2.5305 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8005 2.5827 0.0000 C 0 0 0 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 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 4.2072 1.6691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 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 2 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 1.7321 1.0000 0.0000 C 0 0 1 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 2.8060 2.4781 0.0000 C 0 0 2 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 5.1854 1.4612 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 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 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0559 3.4464 0.0000 O 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 0.0000 -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 2 6 1 0 0 0 0 2 16 1 0 0 0 0 3 17 1 0 0 0 0 4 5 2 0 0 0 0 4 25 1 0 0 0 0 5 13 1 0 0 0 0 6 8 1 0 0 0 0 6 18 1 1 0 0 0 7 3 1 6 0 0 0 7 10 1 0 0 0 0 7 26 1 0 0 0 0 8 5 1 6 0 0 0 8 9 1 0 0 0 0 9 14 1 0 0 0 0 9 16 1 6 0 0 0 10 11 1 0 0 0 0 10 19 1 1 0 0 0 11 12 1 0 0 0 0 11 20 1 6 0 0 0 12 15 1 0 0 0 0 12 21 1 1 0 0 0 13 22 2 0 0 0 0 13 23 1 0 0 0 0 14 25 1 0 0 0 0 14 27 1 1 0 0 0 15 26 1 0 0 0 0 15 27 1 6 0 0 0 16 1 1 6 0 0 0 16 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	392.13
Volume:	351.042
LogP:	-1.076
LogD:	-0.459
LogS:	-0.717
# Rotatable Bonds:	4
TPSA:	186.37
# H-Bond Aceptor:	11
# H-Bond Donor:	7
# Rings:	3
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.256
Synthetic Accessibility Score:	4.894
Fsp3:	0.812
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.503
MDCK Permeability:	0.0001662760623730719
Pgp-inhibitor:	0.0
Pgp-substrate:	0.732
Human Intestinal Absorption (HIA):	0.861
20% Bioavailability (F20%):	0.018
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.246
Plasma Protein Binding (PPB):	20.50454330444336%
Volume Distribution (VD):	0.284
Pgp-substrate:	57.195980072021484%

ADMET: Metabolism

CYP1A2-inhibitor:	0.012
CYP1A2-substrate:	0.045
CYP2C19-inhibitor:	0.013
CYP2C19-substrate:	0.053
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.054
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.088
CYP3A4-inhibitor:	0.014
CYP3A4-substrate:	0.015

ADMET: Excretion

Clearance (CL):	1.316
Half-life (T1/2):	0.874

ADMET: Toxicity

hERG Blockers:	0.057
Human Hepatotoxicity (H-HT):	0.266
Drug-inuced Liver Injury (DILI):	0.763
AMES Toxicity:	0.059
Rat Oral Acute Toxicity:	0.011
Maximum Recommended Daily Dose:	0.006
Skin Sensitization:	0.079
Carcinogencity:	0.922
Eye Corrosion:	0.003
Eye Irritation:	0.073
Respiratory Toxicity:	0.827

Download Data

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

Natural Product: NPC127235

Natural Product ID:	NPC127235
*Common Name:**	Shanzhiside
IUPAC Name:	(1S,4aS,5R,7S,7aS)-5,7-dihydroxy-7-methyl-1-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-4a,5,6,7a-tetrahydro-1H-cyclopenta[c]pyran-4-carboxylic acid
Synonyms:	Shanzhiside
Standard InCHIKey:	YSIFYNVXJOGADM-KDYWOABDSA-N
Standard InCHI:	InChI=1S/C16H24O11/c1-16(24)2-6(18)8-5(13(22)23)4-25-14(9(8)16)27-15-12(21)11(20)10(19)7(3-17)26-15/h4,6-12,14-15,17-21,24H,2-3H2,1H3,(H,22,23)/t6-,7-,8+,9-,10-,11+,12-,14+,15+,16+/m1/s1
SMILES:	OC[C@H]1O[C@@H](O[C@@H]2OC=C([C@@H]3[C@H]2[C@@](C)(O)C[C@H]3O)C(=O)O)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL518392
PubChem CID:	11948668
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0004081] Iridoid 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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32141747]
NPO5652	Barleria lupulina	Species	Acanthaceae	Eukaryota	aerial part	purchased in Vung Tau, Vietnam	2012-MAR	PMID[25611215]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[23305920]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	fruit	n.a.	n.a.	PMID[19650637]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	fruit	n.a.	n.a.	PMID[18505286]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	Seoul, Korea	2000-Jun	PMID[16643034]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[16309325]
NPO5652	Barleria lupulina	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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	1

Activity Type	# Activity
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT35	Others	n.a.		IC50	=	78.6	ug.mL-1	PMID[544759]

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☑ 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 NPC127235 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	226
0.1-0.2	1527
0.2-0.3	5427
0.3-0.4	10526
0.4-0.5	11619
0.5-0.6	7621
0.6-0.7	5206
0.7-0.8	492
0.8-0.85	28
0.85-0.9	9
0.9-0.95	10
0.95-1	6

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Similarity Score	Similarity Level	Natural Product ID
0.9697	High Similarity	NPC197813
0.9697	High Similarity	NPC80338
0.9697	High Similarity	NPC148270
0.9588	High Similarity	NPC3488
0.9588	High Similarity	NPC287539

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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 NPC127235 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	226
0.1-0.2	2119
0.2-0.3	3880
0.3-0.4	1946
0.4-0.5	548
0.5-0.6	281
0.6-0.7	148
0.7-0.8	2
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7241	Intermediate Similarity	NPD6053	Discontinued
0.7236	Intermediate Similarity	NPD7507	Approved
0.7193	Intermediate Similarity	NPD6686	Approved
0.7179	Intermediate Similarity	NPD8133	Approved
0.7105	Intermediate Similarity	NPD6412	Phase 2

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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