NPASS Compound

Structure

NPC207983 OpenBabel06302215162D 53 58 0 0 1 0 0 0 0 0999 V2000 -6.9282 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -5.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.6603 -6.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.5263 -5.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.5263 -4.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.6603 -4.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.7942 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9282 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9282 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9282 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.7942 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.6603 -1.0000 0.0000 O 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 -1.0000 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 -4.3301 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 1 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 -3.4641 -0.0000 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 -1.7321 -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 -3.4641 -1.0000 0.0000 O 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 -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 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -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 -1.7321 -3.0000 0.0000 C 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 -0.8660 -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 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 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 0.8660 0.5000 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 1.5000 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 -5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 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 -10.3923 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 -6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -7.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 53 1 1 0 0 0 4 5 1 0 0 0 0 4 52 1 6 0 0 0 5 6 1 0 0 0 0 5 51 1 6 0 0 0 6 7 1 0 0 0 0 6 8 1 1 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 15 1 0 0 0 0 10 11 1 6 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 13 18 1 1 0 0 0 14 15 1 0 0 0 0 14 17 1 6 0 0 0 15 16 1 6 0 0 0 18 19 1 0 0 0 0 20 19 1 1 0 0 0 20 21 1 0 0 0 0 20 25 1 0 0 0 0 21 22 1 0 0 0 0 21 50 1 1 0 0 0 22 23 1 0 0 0 0 22 49 1 1 0 0 0 23 24 1 0 0 0 0 23 48 1 6 0 0 0 24 25 1 0 0 0 0 24 26 1 1 0 0 0 26 27 1 0 0 0 0 27 37 2 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 28 30 1 0 0 0 0 30 35 2 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 31 47 1 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 46 1 0 0 0 0 34 35 1 0 0 0 0 35 36 1 0 0 0 0 36 37 1 0 0 0 0 37 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 42 44 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	756.21
Volume:	682.698
LogP:	-0.302
LogD:	-0.095
LogS:	-3.183
# Rotatable Bonds:	8
TPSA:	328.35
# H-Bond Aceptor:	20
# H-Bond Donor:	12
# Rings:	6
# Heavy Atoms:	20

MedChem Properties

QED Drug-Likeness Score:	0.103
Synthetic Accessibility Score:	5.398
Fsp3:	0.545
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:	-6.53
MDCK Permeability:	3.6202352930558845e-05
Pgp-inhibitor:	0.011
Pgp-substrate:	0.991
Human Intestinal Absorption (HIA):	0.935
20% Bioavailability (F20%):	0.028
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.084
Plasma Protein Binding (PPB):	84.5990982055664%
Volume Distribution (VD):	0.544
Pgp-substrate:	17.02738380432129%

ADMET: Metabolism

CYP1A2-inhibitor:	0.033
CYP1A2-substrate:	0.036
CYP2C19-inhibitor:	0.031
CYP2C19-substrate:	0.049
CYP2C9-inhibitor:	0.005
CYP2C9-substrate:	0.077
CYP2D6-inhibitor:	0.026
CYP2D6-substrate:	0.103
CYP3A4-inhibitor:	0.031
CYP3A4-substrate:	0.003

ADMET: Excretion

Clearance (CL):	0.725
Half-life (T1/2):	0.783

ADMET: Toxicity

hERG Blockers:	0.353
Human Hepatotoxicity (H-HT):	0.081
Drug-inuced Liver Injury (DILI):	0.982
AMES Toxicity:	0.776
Rat Oral Acute Toxicity:	0.022
Maximum Recommended Daily Dose:	0.001
Skin Sensitization:	0.651
Carcinogencity:	0.1
Eye Corrosion:	0.003
Eye Irritation:	0.251
Respiratory Toxicity:	0.007

Download Data

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

Natural Product: NPC207983

Natural Product ID:	NPC207983
*Common Name:**	PWFJILMZPHBSAY-CZPRTVHTSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PWFJILMZPHBSAY-CZPRTVHTSA-N
Standard InCHI:	InChI=1S/C33H40O20/c1-9-19(38)22(41)25(44)32(48-9)52-28-10(2)49-31(27(46)24(28)43)47-8-17-20(39)23(42)26(45)33(51-17)53-30-21(40)18-15(37)6-12(34)7-16(18)50-29(30)11-3-4-13(35)14(36)5-11/h3-7,9-10,17,19-20,22-28,31-39,41-46H,8H2,1-2H3/t9-,10-,17+,19-,20-,22+,23-,24-,25+,26+,27+,28+,31+,32-,33-/m1/s1
SMILES:	C[C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O[C@H]1[C@@H](C)O[C@@H]([C@H]([C@H]1O)O)OC[C@H]1[C@H]([C@H]([C@@H]([C@H](O1)Oc1c(=O)c2c(cc(cc2oc1c1ccc(c(c1)O)O)O)O)O)O)O)O)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:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003531] Flavonoid-3-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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO26990	Rhizochalina incrustata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[15730256]
NPO25801	Harungana madagascariensis	Species	Hypericaceae	Eukaryota	stem bark	n.a.	n.a.	PMID[16499321]
NPO25801	Harungana madagascariensis	Species	Hypericaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[17352491]
NPO26990	Rhizochalina incrustata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[18052325]
NPO26333	Actinidia arguta	Species	Actinidiaceae	Eukaryota	n.a.	root	n.a.	PMID[18481026]
NPO2937	Pseudoalteromonas rubra	Species	Pseudoalteromonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[18922034]
NPO26547	Uncaria tomentosa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1919590]
NPO26333	Actinidia arguta	Species	Actinidiaceae	Eukaryota	n.a.	root	n.a.	PMID[19336935]
NPO26547	Uncaria tomentosa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2553871]
NPO25801	Harungana madagascariensis	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26727375]
NPO26333	Actinidia arguta	Species	Actinidiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32315181]
NPO26333	Actinidia arguta	Species	Actinidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26547	Uncaria tomentosa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26547	Uncaria tomentosa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26333	Actinidia arguta	Species	Actinidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25801	Harungana madagascariensis	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26333	Actinidia arguta	Species	Actinidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25801	Harungana madagascariensis	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26815	Asteracantha longifolia	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO26990	Rhizochalina incrustata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO27153	Vasconcellea cundinamarcensis	Species	Caricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26547	Uncaria tomentosa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26333	Actinidia arguta	Species	Actinidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26415	Polyporus anthracophilus	Species	Polyporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2937	Pseudoalteromonas rubra	Species	Pseudoalteromonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO26492	Sesamoides canescens	Species	Resedaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14566	Delphinium fangshanense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28220	Streptomyces goshikiensis	Species	Streptomycetaceae	Bacteria	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 NPC207983 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	476
0.1-0.2	1818
0.2-0.3	4119
0.3-0.4	9503
0.4-0.5	8326
0.5-0.6	5219
0.6-0.7	5822
0.7-0.8	5018
0.8-0.85	1399
0.85-0.9	492
0.9-0.95	418
0.95-1	87

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 NPC207983 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	416
0.1-0.2	960
0.2-0.3	2077
0.3-0.4	2716
0.4-0.5	1794
0.5-0.6	804
0.6-0.7	256
0.7-0.8	93
0.8-0.85	21
0.85-0.9	5
0.9-0.95	5
0.95-1	3

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