NPASS Compound

Structure

NPC22994 OpenBabel06302215102D 46 51 0 0 1 0 0 0 0 0999 V2000 -2.3603 0.7315 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7030 0.0010 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.0069 -0.9335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9682 -1.1375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2721 -2.0721 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.6148 -2.8025 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4108 -3.7638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3453 -3.4599 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6535 -2.5985 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2334 -2.2761 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8518 0.4921 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8509 1.4748 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0006 1.9661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8515 0.4913 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7227 0.9939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7033 -0.0008 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5554 0.4908 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4072 -0.0013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4069 -0.9851 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2584 -1.4767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1295 -0.9741 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1294 -1.9795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2579 -2.4599 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4058 -2.9515 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5543 -2.4599 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5549 -1.4767 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7028 -1.9683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7031 -0.9846 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8515 -1.4759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 -0.9837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8711 -0.5026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1286 -2.9631 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5557 1.4745 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5394 1.4742 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.0315 2.3260 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0152 2.3257 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.5068 1.4736 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0147 0.6219 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.5063 -0.2302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4900 -0.2305 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0310 0.6222 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4905 1.4733 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5073 3.1775 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5399 3.1780 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7167 1.9753 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 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 5 10 1 6 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 6 9 1 0 0 0 0 11 2 1 1 0 0 0 11 12 1 0 0 0 0 11 31 1 0 0 0 0 12 13 1 0 0 0 0 12 46 1 1 0 0 0 13 14 1 0 0 0 0 14 31 1 0 0 0 0 14 15 1 6 0 0 0 14 16 1 0 0 0 0 16 17 1 0 0 0 0 16 28 1 0 0 0 0 17 18 1 0 0 0 0 17 34 1 1 0 0 0 19 18 1 1 0 0 0 19 20 1 0 0 0 0 19 26 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 23 33 1 1 0 0 0 24 25 1 0 0 0 0 26 25 1 6 0 0 0 26 28 1 0 0 0 0 26 27 1 0 0 0 0 28 27 1 1 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 1 0 0 0 35 34 1 1 0 0 0 35 36 1 0 0 0 0 35 42 1 0 0 0 0 36 37 1 0 0 0 0 36 45 1 6 0 0 0 37 38 1 0 0 0 0 37 44 1 1 0 0 0 38 39 1 0 0 0 0 38 43 1 6 0 0 0 39 40 1 1 0 0 0 39 42 1 0 0 0 0 40 41 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	654.43
Volume:	667.775
LogP:	3.191
LogD:	3.177
LogS:	-3.162
# Rotatable Bonds:	8
TPSA:	180.3
# H-Bond Aceptor:	10
# H-Bond Donor:	8
# Rings:	6
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.181
Synthetic Accessibility Score:	6.419
Fsp3:	1.0
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:	-5.924
MDCK Permeability:	2.4045795726124197e-05
Pgp-inhibitor:	0.052
Pgp-substrate:	0.883
Human Intestinal Absorption (HIA):	0.594
20% Bioavailability (F20%):	0.637
30% Bioavailability (F30%):	0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.088
Plasma Protein Binding (PPB):	58.18733596801758%
Volume Distribution (VD):	0.433
Pgp-substrate:	10.312789916992188%

ADMET: Metabolism

CYP1A2-inhibitor:	0.002
CYP1A2-substrate:	0.126
CYP2C19-inhibitor:	0.002
CYP2C19-substrate:	0.674
CYP2C9-inhibitor:	0.006
CYP2C9-substrate:	0.047
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.067
CYP3A4-inhibitor:	0.707
CYP3A4-substrate:	0.159

ADMET: Excretion

Clearance (CL):	1.375
Half-life (T1/2):	0.577

ADMET: Toxicity

hERG Blockers:	0.118
Human Hepatotoxicity (H-HT):	0.316
Drug-inuced Liver Injury (DILI):	0.012
AMES Toxicity:	0.055
Rat Oral Acute Toxicity:	0.843
Maximum Recommended Daily Dose:	0.964
Skin Sensitization:	0.862
Carcinogencity:	0.059
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.978

Download Data

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

Natural Product: NPC22994

Natural Product ID:	NPC22994
*Common Name:**	GYNPLPULVIGPCZ-MLHRCHTDSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GYNPLPULVIGPCZ-MLHRCHTDSA-N
Standard InCHI:	InChI=1S/C36H62O10/c1-18(8-9-24(40)32(4,5)44)25-19(38)15-34(7)29-20(45-30-28(43)27(42)26(41)21(16-37)46-30)14-22-31(2,3)23(39)10-11-35(22)17-36(29,35)13-12-33(25,34)6/h18-30,37-44H,8-17H2,1-7H3/t18-,19+,20+,21-,22+,23+,24-,25+,26-,27+,28-,29+,30-,33-,34+,35-,36+/m1/s1
SMILES:	C[C@H](CC[C@H](C(C)(C)O)O)[C@H]1[C@H](C[C@@]2(C)[C@@H]3[C@H](C[C@H]4C(C)(C)[C@H](CC[C@]54C[C@@]35CC[C@]12C)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	102263731
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds]

*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
NPO17157	Agrostistachys hookeri	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3373221]
NPO18479	Dysoxylum lenticellare	Species	Meliaceae	Eukaryota	leaves	n.a.	n.a.	PMID[3443856]
NPO6935	Microsorum punctatum	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17157	Agrostistachys hookeri	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12449	Silene linicola	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16017	Dryadodaphne novoguineensis	Species	Atherospermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18479	Dysoxylum lenticellare	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19740	Sinularia firma	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1328	Eria marginata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6935	Microsorum punctatum	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10744	Astropecten latespinosus	Species	Astropectinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18209	Lathyrus rotundifolius	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27673	Sarcopyramis nepalensis	Species	Melastomataceae	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 NPC22994 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	569
0.1-0.2	5028
0.2-0.3	13373
0.3-0.4	10477
0.4-0.5	5516
0.5-0.6	3922
0.6-0.7	2490
0.7-0.8	985
0.8-0.85	133
0.85-0.9	160
0.9-0.95	43
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 NPC22994 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	550
0.1-0.2	4579
0.2-0.3	2823
0.3-0.4	622
0.4-0.5	288
0.5-0.6	228
0.6-0.7	43
0.7-0.8	15
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
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