NPASS Compound

Structure

NPC133789 OpenBabel06302216012D 58 63 0 0 1 0 0 0 0 0999 V2000 -9.5263 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -3.5000 0.0000 C 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 -2.0000 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 -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 2 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 3.0000 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 -4.3301 2.5000 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 -5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 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 -6.0622 -0.5000 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 -6.9282 0.0000 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 -2.5981 -0.5000 0.0000 C 0 0 2 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 -2.0000 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 -4.3301 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 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 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -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 -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 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 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -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 0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 8.5000 0.0000 C 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 -7.7942 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 58 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 57 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 25 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 23 1 0 0 0 0 13 12 1 6 0 0 0 13 14 1 0 0 0 0 13 28 1 0 0 0 0 14 20 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 19 27 1 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 28 29 1 1 0 0 0 28 39 1 0 0 0 0 29 35 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 31 32 1 0 0 0 0 31 33 1 0 0 0 0 33 34 2 0 0 0 0 34 35 1 0 0 0 0 34 56 1 0 0 0 0 35 36 1 0 0 0 0 36 37 2 0 0 0 0 36 38 1 0 0 0 0 38 43 2 0 0 0 0 38 39 1 0 0 0 0 39 40 2 0 0 0 0 40 41 1 0 0 0 0 41 42 2 0 0 0 0 41 45 1 0 0 0 0 42 43 1 0 0 0 0 43 44 1 0 0 0 0 45 46 1 0 0 0 0 46 47 1 0 0 0 0 47 48 2 0 0 0 0 48 49 1 0 0 0 0 48 50 1 0 0 0 0 50 51 1 0 0 0 0 51 52 1 0 0 0 0 52 53 2 0 0 0 0 53 54 1 0 0 0 0 53 55 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	782.38
Volume:	844.883
LogP:	12.071
LogD:	5.727
LogS:	-1.58
# Rotatable Bonds:	13
TPSA:	139.84
# H-Bond Aceptor:	8
# H-Bond Donor:	6
# Rings:	6
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.05
Synthetic Accessibility Score:	3.746
Fsp3:	0.28
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.783
MDCK Permeability:	1.0035681043518707e-05
Pgp-inhibitor:	0.288
Pgp-substrate:	0.15
Human Intestinal Absorption (HIA):	0.916
20% Bioavailability (F20%):	0.999
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0
Plasma Protein Binding (PPB):	97.14910888671875%
Volume Distribution (VD):	0.1
Pgp-substrate:	4.067647457122803%

ADMET: Metabolism

CYP1A2-inhibitor:	0.802
CYP1A2-substrate:	0.18
CYP2C19-inhibitor:	0.891
CYP2C19-substrate:	0.048
CYP2C9-inhibitor:	0.656
CYP2C9-substrate:	0.961
CYP2D6-inhibitor:	0.333
CYP2D6-substrate:	0.786
CYP3A4-inhibitor:	0.024
CYP3A4-substrate:	0.021

ADMET: Excretion

Clearance (CL):	5.062
Half-life (T1/2):	0.01

ADMET: Toxicity

hERG Blockers:	0.065
Human Hepatotoxicity (H-HT):	0.962
Drug-inuced Liver Injury (DILI):	0.945
AMES Toxicity:	0.184
Rat Oral Acute Toxicity:	0.03
Maximum Recommended Daily Dose:	0.989
Skin Sensitization:	0.971
Carcinogencity:	0.018
Eye Corrosion:	0.003
Eye Irritation:	0.923
Respiratory Toxicity:	0.38

Download Data

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

Natural Product: NPC133789

Natural Product ID:	NPC133789
*Common Name:**	XBUDJYQWKSZGTP-BKQXBYFJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XBUDJYQWKSZGTP-BKQXBYFJSA-N
Standard InCHI:	InChI=1S/C50H54O8/c1-27(2)11-9-13-29(5)15-17-57-33-23-37-43(35-19-31(7)21-39(51)45(35)49(55)47(37)41(53)25-33)44-36-20-32(8)22-40(52)46(36)50(56)48-38(44)24-34(26-42(48)54)58-18-16-30(6)14-10-12-28(3)4/h11-12,15-16,19-26,43-44,51-54H,9-10,13-14,17-18H2,1-8H3/b29-15+,30-16+/t43-,44+
SMILES:	CC(=CCC/C(=C/COc1cc2[C@H](c3cc(C)cc(c3C(=O)c2c(c1)O)O)[C@@H]1c2cc(C)cc(c2C(=O)c2c1cc(cc2O)OC/C=C(C)/CCC=C(C)C)O)/C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11181897
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000018] Anthracenes

*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
NPO12096	Psorospermum febrifugum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19191562]
NPO11207	Wilbrandia ebracteata	Species	Cucurbitaceae	Eukaryota	n.a.	root	n.a.	PMID[20678557]
NPO9680	Ajuga ciliata	Species	Lamiaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[21682262]
NPO9680	Ajuga ciliata	Species	Lamiaceae	Eukaryota	whole plants	Zhejiang Province, China	2008-AUG	PMID[21682262]
NPO12096	Psorospermum febrifugum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7189773]
NPO12096	Psorospermum febrifugum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9680	Ajuga ciliata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12096	Psorospermum febrifugum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9680	Ajuga ciliata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1645	Sticta pulmonaria	Species	Lobariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10519	Angylocalyx vermeulenii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7544	Squalus wakiyae	Species	Squalidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5103	Lobelia berlandieri	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12096	Psorospermum febrifugum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15236	Leucetta avocado	Species	Leucettidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11207	Wilbrandia ebracteata	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13912	Delphinium gracile	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26692	Lophium arboricola	Species	Mytilinidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1478	Trichoptilus wahlbergi	Species	Pterophoridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1108	Aralia decaisneana	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22203	Tapinella panuoides	Species	Tapinellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9680	Ajuga ciliata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15613	Clerodendrum uncinatum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4475	Erythrina costaricensis	Species	Fabaceae	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 NPC133789 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	422
0.1-0.2	1635
0.2-0.3	3459
0.3-0.4	9300
0.4-0.5	9624
0.5-0.6	3704
0.6-0.7	5506
0.7-0.8	5874
0.8-0.85	2273
0.85-0.9	780
0.9-0.95	119
0.95-1	1

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 NPC133789 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	373
0.1-0.2	1015
0.2-0.3	1579
0.3-0.4	2624
0.4-0.5	1936
0.5-0.6	1005
0.6-0.7	415
0.7-0.8	160
0.8-0.85	35
0.85-0.9	6
0.9-0.95	1
0.95-1	1

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