NPASS Compound

Structure

CID90822 OpenBabel06191715432D 52 61 0 0 1 0 0 0 0 0999 V2000 3.0574 0.9543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4763 0.1351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8295 -4.4268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7287 -4.9331 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7529 -1.3533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7529 0.2851 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5304 1.7735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9493 0.9543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1219 -5.3265 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4364 -5.8328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6988 -1.3533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6988 0.2851 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6278 -3.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5685 -0.7102 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2663 -3.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0650 -0.0172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3286 -2.1084 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5304 0.1351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0957 -4.2302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2799 -0.5341 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4763 1.7735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4889 -6.0295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1718 -0.5341 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4470 -4.4194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4836 -0.2424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6278 -3.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2557 -1.0682 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2438 -1.6407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2663 -3.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6278 -0.2040 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0159 -2.4664 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4470 -2.5275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6278 -0.8642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6437 -1.6022 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 -2.7965 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3880 -2.2624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3880 -1.6022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0682 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8251 -1.4154 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5845 -1.5034 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3880 -3.3305 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3880 -0.5341 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.9493 2.5927 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7812 -6.9291 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1177 -0.5341 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4470 -6.3112 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2489 0.3136 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 -1.0847 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8676 -0.4704 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9692 -2.3675 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 -1.0159 -3.1265 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 7 1 0 0 0 0 1 18 2 0 0 0 0 2 8 2 0 0 0 0 2 18 1 0 0 0 0 3 9 1 0 0 0 0 3 19 2 0 0 0 0 4 10 2 0 0 0 0 4 19 1 0 0 0 0 5 11 1 0 0 0 0 5 20 2 0 0 0 0 6 12 2 0 0 0 0 6 20 1 0 0 0 0 7 21 2 0 0 0 0 8 21 1 0 0 0 0 9 22 2 0 0 0 0 10 22 1 0 0 0 0 11 23 2 0 0 0 0 12 23 1 0 0 0 0 13 24 2 0 0 0 0 13 26 1 0 0 0 0 14 25 2 0 0 0 0 14 27 1 0 0 0 0 15 24 1 0 0 0 0 15 29 2 0 0 0 0 16 25 1 0 0 0 0 16 30 2 0 0 0 0 17 28 1 0 0 0 0 17 31 2 0 0 0 0 21 43 1 0 0 0 0 22 44 1 0 0 0 0 23 45 1 0 0 0 0 24 46 1 0 0 0 0 25 47 1 0 0 0 0 26 32 2 0 0 0 0 27 33 2 0 0 0 0 28 39 1 0 0 0 0 28 48 2 0 0 0 0 29 32 1 0 0 0 0 29 50 1 0 0 0 0 30 33 1 0 0 0 0 30 51 1 0 0 0 0 31 36 1 0 0 0 0 31 52 1 0 0 0 0 32 34 1 0 0 0 0 34 27 1 1 0 0 0 34 40 1 0 0 0 0 35 26 1 1 0 0 0 35 36 1 0 0 0 0 35 41 1 0 0 0 0 36 37 2 0 0 0 0 37 38 1 0 0 0 0 37 39 1 0 0 0 0 38 33 1 6 0 0 0 38 42 1 0 0 0 0 39 49 2 0 0 0 0 40 18 1 6 0 0 0 40 50 1 0 0 0 0 41 19 1 6 0 0 0 41 52 1 0 0 0 0 42 20 1 1 0 0 0 42 51 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	692.17
Volume:	687.233
LogP:	7.0
LogD:	3.808
LogS:	-3.897
# Rotatable Bonds:	3
TPSA:	173.21
# H-Bond Aceptor:	10
# H-Bond Donor:	7
# Rings:	10
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.089
Synthetic Accessibility Score:	5.062
Fsp3:	0.095
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:	-6.032
MDCK Permeability:	7.537541023339145e-06
Pgp-inhibitor:	0.162
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.809
20% Bioavailability (F20%):	0.712
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001
Plasma Protein Binding (PPB):	97.72379302978516%
Volume Distribution (VD):	0.462
Pgp-substrate:	2.804764986038208%

ADMET: Metabolism

CYP1A2-inhibitor:	0.075
CYP1A2-substrate:	0.441
CYP2C19-inhibitor:	0.949
CYP2C19-substrate:	0.046
CYP2C9-inhibitor:	0.743
CYP2C9-substrate:	0.993
CYP2D6-inhibitor:	0.057
CYP2D6-substrate:	0.813
CYP3A4-inhibitor:	0.193
CYP3A4-substrate:	0.233

ADMET: Excretion

Clearance (CL):	7.392
Half-life (T1/2):	0.224

ADMET: Toxicity

hERG Blockers:	0.039
Human Hepatotoxicity (H-HT):	0.364
Drug-inuced Liver Injury (DILI):	0.983
AMES Toxicity:	0.571
Rat Oral Acute Toxicity:	0.975
Maximum Recommended Daily Dose:	0.81
Skin Sensitization:	0.803
Carcinogencity:	0.053
Eye Corrosion:	0.003
Eye Irritation:	0.892
Respiratory Toxicity:	0.023

Download Data

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

Natural Product: NPC90822

Natural Product ID:	NPC90822
*Common Name:**	Hopeanolin
IUPAC Name:	n.a.
Synonyms:	Hopeanolin
Standard InCHIKey:	PEVCENMPFGEBKL-MGZRWOOSSA-N
Standard InCHI:	InChI=1S/C42H28O10/c43-21-7-1-18(2-8-21)40-34-27-14-25(47)16-30-33(27)38(42(51-30)20-5-11-23(45)12-6-20)37-36-31(17-28(48)39(37)49)52-41(19-3-9-22(44)10-4-19)35(36)26-13-24(46)15-29(50-40)32(26)34/h1-17,34-35,38,40-47H/t34-,35-,38-,40+,41+,42-/m1/s1
SMILES:	Oc1ccc(cc1)[C@@H]1OC2=CC(=O)C(=O)C3=C2[C@H]1c1cc(O)cc2c1[C@H]([C@@H](O2)c1ccc(cc1)O)c1c2[C@H]3[C@H](Oc2cc(c1)O)c1ccc(cc1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL502987
PubChem CID:	16099540
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0003405] 2-arylbenzofuran flavonoids

*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
NPO14000	Hopea exalata	Species	Dipterocarpaceae	Eukaryota	stem bark	Botanical Garden at Jianfeng Town, Ledong County, Hainan Province, China	2004-JUL	PMID[17190464]
NPO16805	Senecio cisplatinus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16691	Viguiera radula	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13778	Melandrium turkestanicum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO14476	Sterculia alata	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2042	Garcinia bancana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14958	Duguetia eximia	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17995	Xeromphis spinosa	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO14000	Hopea exalata	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2042	Garcinia bancana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]

Showing 1 to 10 of 11 entries

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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
MIC	6

Activity Type	# Activity
Organism	6

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT826	Organism	Magnaporthe oryzae	Magnaporthe oryzae	MIC	=	0.1	ug.mL-1	PMID[506680]
NPT1199	Organism	Valsa mali	Valsa mali	MIC	=	1.55	ug.mL-1	PMID[506680]
NPT2705	Organism	Alternaria solani	Alternaria solani	MIC	=	1.56	ug.mL-1	PMID[506680]
NPT2648	Organism	Fusarium oxysporum f. sp. vasinfectum	Fusarium oxysporum f. sp. vasinfectum	MIC	=	6.22	ug.mL-1	PMID[506680]
NPT2637	Organism	Colletotrichum lagenarium	Colletotrichum lagenarium	MIC	=	10.6	ug.mL-1	PMID[506680]
NPT962	Organism	Alternaria alternata	Alternaria alternata	MIC	=	22.5	ug.mL-1	PMID[506680]

Showing 1 to 6 of 6 entries

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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 NPC90822 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	419
0.1-0.2	1614
0.2-0.3	3115
0.3-0.4	8093
0.4-0.5	11076
0.5-0.6	4041
0.6-0.7	7053
0.7-0.8	6981
0.8-0.85	265
0.85-0.9	39
0.9-0.95	0
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.8954	High Similarity	NPC176804
0.8954	High Similarity	NPC71686
0.8889	High Similarity	NPC149633
0.8827	High Similarity	NPC261896
0.8802	High Similarity	NPC300657

Showing 1 to 5 of 200 entries

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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 NPC90822 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	366
0.1-0.2	920
0.2-0.3	1549
0.3-0.4	2667
0.4-0.5	2032
0.5-0.6	1075
0.6-0.7	422
0.7-0.8	116
0.8-0.85	3
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
0.8204	Intermediate Similarity	NPD6959	Discontinued
0.8121	Intermediate Similarity	NPD8443	Clinical (unspecified phase)
0.7917	Intermediate Similarity	NPD3749	Approved
0.7875	Intermediate Similarity	NPD3750	Approved
0.7857	Intermediate Similarity	NPD4868	Clinical (unspecified phase)

Showing 1 to 5 of 200 entries

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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