NPASS Compound

Structure

NPC6788 OpenBabel06302215562D 35 39 0 0 1 0 0 0 0 0999 V2000 3.2389 0.4274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3200 0.6733 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0735 1.5921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6475 0.0005 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6478 -0.9508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8248 -1.4269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0003 -0.9513 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8239 -1.4274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6484 -0.9517 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6487 -0.0005 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3418 -0.9786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8245 0.4757 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8248 1.4275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6492 1.9032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4735 1.4271 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.2974 1.9027 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4510 2.3920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2979 2.8541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1221 3.3293 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.9457 2.8532 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.9452 1.9018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9316 1.9012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4379 1.0473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1210 1.4266 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1207 0.4747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2968 -0.0009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4732 0.4752 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4729 -0.5024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8003 3.3459 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1227 4.3157 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0005 -1.9025 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8684 -2.2897 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7703 -2.4614 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6392 -2.0743 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 4 31 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 31 1 0 0 0 0 7 8 1 0 0 0 0 7 32 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 27 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 12 31 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 27 1 0 0 0 0 16 24 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 30 1 0 0 0 0 20 21 1 0 0 0 0 20 29 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 21 24 1 0 0 0 0 24 25 1 1 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 1 0 0 0 32 33 2 0 0 0 0 32 34 1 0 0 0 0 34 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	486.37
Volume:	531.838
LogP:	5.411
LogD:	5.226
LogS:	-5.613
# Rotatable Bonds:	3
TPSA:	66.76
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.363
Synthetic Accessibility Score:	4.896
Fsp3:	0.903
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-5.211
MDCK Permeability:	5.510329356184229e-05
Pgp-inhibitor:	0.568
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.062
30% Bioavailability (F30%):	0.856

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.007
Plasma Protein Binding (PPB):	89.56659698486328%
Volume Distribution (VD):	0.844
Pgp-substrate:	3.63733172416687%

ADMET: Metabolism

CYP1A2-inhibitor:	0.025
CYP1A2-substrate:	0.558
CYP2C19-inhibitor:	0.06
CYP2C19-substrate:	0.931
CYP2C9-inhibitor:	0.249
CYP2C9-substrate:	0.34
CYP2D6-inhibitor:	0.01
CYP2D6-substrate:	0.668
CYP3A4-inhibitor:	0.626
CYP3A4-substrate:	0.483

ADMET: Excretion

Clearance (CL):	3.651
Half-life (T1/2):	0.199

ADMET: Toxicity

hERG Blockers:	0.266
Human Hepatotoxicity (H-HT):	0.321
Drug-inuced Liver Injury (DILI):	0.022
AMES Toxicity:	0.002
Rat Oral Acute Toxicity:	0.287
Maximum Recommended Daily Dose:	0.831
Skin Sensitization:	0.449
Carcinogencity:	0.007
Eye Corrosion:	0.015
Eye Irritation:	0.041
Respiratory Toxicity:	0.921

Download Data

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

Natural Product: NPC6788

Natural Product ID:	NPC6788
*Common Name:**	ZYVYVSDVVCCWKV-HCMYPKGDSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZYVYVSDVVCCWKV-HCMYPKGDSA-N
Standard InCHI:	InChI=1S/C31H50O4/c1-18(2)19-11-14-31(26(34)35-8)16-15-29(6)20(24(19)31)9-10-23-28(5)17-21(32)25(33)27(3,4)22(28)12-13-30(23,29)7/h19-25,32-33H,1,9-17H2,2-8H3/t19-,20+,21+,22-,23+,24+,25+,28-,29+,30+,31-/m0/s1
SMILES:	C=C(C)[C@@H]1CC[C@@]2(CC[C@]3(C)[C@H](CC[C@@H]4[C@@]5(C)C[C@H]([C@H](C(C)(C)[C@@H]5CC[C@@]34C)O)O)[C@@H]12)C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	21672694
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO14923	Mollinedia costaricensis	Species	Monimiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21401141]
NPO20393	Hypolepis punctata	Species	Dennstaedtiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20393	Hypolepis punctata	Species	Dennstaedtiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8062	Phlomoides hamosa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18206	Centaurea horrida	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13728	Metanarthecium luteoviride	Species	Nartheciaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21129	Asterias glacialis	Species	Asteriidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20393	Hypolepis punctata	Species	Dennstaedtiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14923	Mollinedia costaricensis	Species	Monimiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18276	Uvaria kirkii	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15823	Maytenus buxifolia	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18958	Podolepis longipedata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19962	Laetiporus versisporus	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21513	Astilbe myriantha	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21399	Diaphus suborbitalis	Species	Myctophidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19643	Dendrodoris krebsii	Species	Dendrodorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8768	Koompassia malaccensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13071	Sindora wallichii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19742	Pluchea lanceolata	Species	Asteraceae	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 NPC6788 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	202
0.1-0.2	1608
0.2-0.3	5953
0.3-0.4	15611
0.4-0.5	6611
0.5-0.6	5066
0.6-0.7	4465
0.7-0.8	2740
0.8-0.85	350
0.85-0.9	54
0.9-0.95	27
0.95-1	10

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 NPC6788 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	180
0.1-0.2	2002
0.2-0.3	4058
0.3-0.4	1974
0.4-0.5	494
0.5-0.6	170
0.6-0.7	173
0.7-0.8	89
0.8-0.85	8
0.85-0.9	0
0.9-0.95	2
0.95-1	0

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