NPASS Compound

Structure

NPC302286 OpenBabel07101718192D 37 40 0 0 1 0 0 0 0 0999 V2000 -3.4263 0.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 0.0000 0.0000 C 0 0 0 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 5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 2.0000 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 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2709 -0.5000 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 6.0622 0.5000 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 1.7321 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.6831 -1.3090 0.0000 C 0 0 2 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 1.7321 3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 3.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 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 -2.6831 0.3090 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 -2.9921 -2.2601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4752 1.2872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3253 -1.9135 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 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 3.4641 2.0000 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 -0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 33 1 0 0 0 0 3 6 1 0 0 0 0 3 13 2 0 0 0 0 4 7 2 0 0 0 0 4 13 1 0 0 0 0 5 8 2 0 0 0 0 5 13 1 0 0 0 0 6 14 2 0 0 0 0 7 14 1 0 0 0 0 8 17 1 0 0 0 0 9 10 2 0 0 0 0 9 25 1 0 0 0 0 10 34 1 0 0 0 0 11 16 1 0 0 0 0 11 24 1 0 0 0 0 12 35 1 0 0 0 0 14 33 1 0 0 0 0 15 12 1 1 0 0 0 15 18 1 0 0 0 0 15 36 1 0 0 0 0 16 25 1 6 0 0 0 16 26 1 0 0 0 0 17 27 2 0 0 0 0 17 35 1 0 0 0 0 18 19 1 0 0 0 0 18 28 1 6 0 0 0 19 20 1 0 0 0 0 19 29 1 1 0 0 0 20 22 1 0 0 0 0 20 30 1 6 0 0 0 21 23 1 0 0 0 0 21 24 1 1 0 0 0 21 25 1 0 0 0 0 22 36 1 0 0 0 0 22 37 1 1 0 0 0 23 34 1 0 0 0 0 23 37 1 6 0 0 0 24 1 1 1 0 0 0 24 31 1 0 0 0 0 25 32 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	524.19
Volume:	496.394
LogP:	0.751
LogD:	-0.108
LogS:	-3.377
# Rotatable Bonds:	8
TPSA:	184.6
# H-Bond Aceptor:	12
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.185
Synthetic Accessibility Score:	4.824
Fsp3:	0.56
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:	-5.904
MDCK Permeability:	7.441781781380996e-05
Pgp-inhibitor:	0.003
Pgp-substrate:	0.995
Human Intestinal Absorption (HIA):	0.884
20% Bioavailability (F20%):	0.086
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.123
Plasma Protein Binding (PPB):	52.76409912109375%
Volume Distribution (VD):	0.392
Pgp-substrate:	24.8800048828125%

ADMET: Metabolism

CYP1A2-inhibitor:	0.024
CYP1A2-substrate:	0.225
CYP2C19-inhibitor:	0.034
CYP2C19-substrate:	0.164
CYP2C9-inhibitor:	0.011
CYP2C9-substrate:	0.201
CYP2D6-inhibitor:	0.026
CYP2D6-substrate:	0.133
CYP3A4-inhibitor:	0.521
CYP3A4-substrate:	0.087

ADMET: Excretion

Clearance (CL):	1.303
Half-life (T1/2):	0.568

ADMET: Toxicity

hERG Blockers:	0.297
Human Hepatotoxicity (H-HT):	0.288
Drug-inuced Liver Injury (DILI):	0.042
AMES Toxicity:	0.181
Rat Oral Acute Toxicity:	0.209
Maximum Recommended Daily Dose:	0.388
Skin Sensitization:	0.437
Carcinogencity:	0.714
Eye Corrosion:	0.003
Eye Irritation:	0.029
Respiratory Toxicity:	0.969

Download Data

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

Natural Product: NPC302286

Natural Product ID:	NPC302286
*Common Name:**	6'-O-E-Para-Methoxycinnamoylharpagide
IUPAC Name:	[(2R,3S,4S,5R,6S)-6-[[(1S,4aS,5R,7S,7aR)-4a,5,7-trihydroxy-7-methyl-1,5,6,7a-tetrahydrocyclopenta[c]pyran-1-yl]oxy]-3,4,5-trihydroxyoxan-2-yl]methyl (E)-3-(4-methoxyphenyl)prop-2-enoate
Synonyms:
Standard InCHIKey:	FLGNDYLGJFFGQZ-HWOKHOLDSA-N
Standard InCHI:	InChI=1S/C25H32O12/c1-24(31)11-16(26)25(32)9-10-34-23(21(24)25)37-22-20(30)19(29)18(28)15(36-22)12-35-17(27)8-5-13-3-6-14(33-2)7-4-13/h3-10,15-16,18-23,26,28-32H,11-12H2,1-2H3/b8-5+/t15-,16-,18-,19+,20-,21-,22+,23+,24+,25-/m1/s1
SMILES:	C[C@@]1(C[C@H]([C@@]2(C=CO[C@H]([C@H]12)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](COC(=O)/C=C/c2ccc(cc2)OC)O1)O)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL518566
PubChem CID:	10984208
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

Show entries

Search:

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	roots	n.a.	n.a.	PMID[12444706]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

Showing 1 to 6 of 6 entries

Previous1Next

☑ 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

Show entries

Search:

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

Showing 0 to 0 of 0 entries

PreviousNext

☑ 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
Others	3

Activity Type	# Activity
Others	3

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified	""	Activity	=	60.3	%	PMID[549148]
NPT2	Others	Unspecified	""	Activity	=	60.9	%	PMID[549148]
NPT2	Others	Unspecified	""	Activity	=	39.1	%	PMID[549148]

Showing 1 to 3 of 3 entries

Previous1Next

☑ 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 NPC302286 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	291
0.1-0.2	1224
0.2-0.3	3006
0.3-0.4	7048
0.4-0.5	10755
0.5-0.6	8923
0.6-0.7	9561
0.7-0.8	1686
0.8-0.85	143
0.85-0.9	38
0.9-0.95	14
0.95-1	8

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC263397
1.0	High Similarity	NPC88754
1.0	High Similarity	NPC237872
1.0	High Similarity	NPC116104
0.9783	High Similarity	NPC37838

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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 NPC302286 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	238
0.1-0.2	735
0.2-0.3	1712
0.3-0.4	2787
0.4-0.5	2106
0.5-0.6	1196
0.6-0.7	339
0.7-0.8	36
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8385	Intermediate Similarity	NPD7685	Pre-registration
0.7973	Intermediate Similarity	NPD7266	Discontinued
0.7806	Intermediate Similarity	NPD1653	Approved
0.7786	Intermediate Similarity	NPD1091	Approved
0.7703	Intermediate Similarity	NPD6653	Approved

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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