NPASS Compound

Structure

NPC319517 OpenBabel06302215362D 92 91 0 0 1 0 0 0 0 0999 V2000 -14.5885 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.7224 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.8564 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.9904 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.1244 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.2583 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.3923 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5263 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6603 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7942 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9282 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7321 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1340 -2.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.1340 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -0.0000 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 2.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 1.0000 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 -0.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.7321 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.0000 1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 2.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5000 2.5981 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 2.5000 1.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5000 2.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5000 3.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3660 4.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3660 5.0981 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 4.2321 5.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2321 6.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0981 7.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9641 6.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0981 8.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9641 8.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9641 9.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8301 10.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8301 11.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6962 11.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6962 12.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5622 13.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5622 14.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4282 14.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4282 15.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.2942 16.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.2942 17.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.1603 17.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.1603 18.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5000 5.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5000 6.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3660 7.0981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6340 7.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6340 8.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5000 8.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5000 9.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3660 10.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3660 11.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2321 11.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2321 12.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0981 13.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0981 14.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9641 14.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9641 15.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8301 16.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8301 17.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6962 17.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 2.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5981 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0622 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9282 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7942 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.6603 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.5263 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.3923 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.2583 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.1244 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.9904 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.8564 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 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 1 0 0 0 0 7 8 2 3 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 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 16 17 2 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 20 21 1 0 0 0 0 20 75 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 23 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 28 74 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 31 34 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 36 56 1 0 0 0 0 37 38 1 0 0 0 0 38 39 1 0 0 0 0 39 40 2 0 0 0 0 39 41 1 0 0 0 0 41 42 1 0 0 0 0 42 43 1 0 0 0 0 43 44 1 0 0 0 0 44 45 1 0 0 0 0 45 46 1 0 0 0 0 46 47 1 0 0 0 0 47 48 1 0 0 0 0 48 49 2 3 0 0 0 49 50 1 0 0 0 0 50 51 1 0 0 0 0 51 52 1 0 0 0 0 52 53 1 0 0 0 0 53 54 1 0 0 0 0 54 55 1 0 0 0 0 56 57 1 0 0 0 0 57 58 2 0 0 0 0 57 59 1 0 0 0 0 59 60 1 0 0 0 0 60 61 1 0 0 0 0 61 62 1 0 0 0 0 62 63 1 0 0 0 0 63 64 1 0 0 0 0 64 65 1 0 0 0 0 65 66 1 0 0 0 0 66 67 2 3 0 0 0 67 68 1 0 0 0 0 68 69 1 0 0 0 0 69 70 1 0 0 0 0 70 71 1 0 0 0 0 71 72 1 0 0 0 0 72 73 1 0 0 0 0 75 76 1 0 0 0 0 76 77 2 0 0 0 0 76 78 1 0 0 0 0 78 79 1 0 0 0 0 79 80 1 0 0 0 0 80 81 1 0 0 0 0 81 82 1 0 0 0 0 82 83 1 0 0 0 0 83 84 1 0 0 0 0 84 85 1 0 0 0 0 85 86 2 3 0 0 0 86 87 1 0 0 0 0 87 88 1 0 0 0 0 88 89 1 0 0 0 0 89 90 1 0 0 0 0 90 91 1 0 0 0 0 91 92 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	1344.91
Volume:	1439.16
LogP:	16.576
LogD:	5.633
LogS:	-3.738
# Rotatable Bonds:	74
TPSA:	230.63
# H-Bond Aceptor:	17
# H-Bond Donor:	1
# Rings:	0
# Heavy Atoms:	19

MedChem Properties

QED Drug-Likeness Score:	0.02
Synthetic Accessibility Score:	5.463
Fsp3:	0.836
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
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:	-5.016
MDCK Permeability:	1.9101180441793986e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.948
Human Intestinal Absorption (HIA):	0.03
20% Bioavailability (F20%):	0.486
30% Bioavailability (F30%):	0.914

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0
Plasma Protein Binding (PPB):	120.0597152709961%
Volume Distribution (VD):	0.612
Pgp-substrate:	0.5871708393096924%

ADMET: Metabolism

CYP1A2-inhibitor:	0.005
CYP1A2-substrate:	0.047
CYP2C19-inhibitor:	0.088
CYP2C19-substrate:	0.019
CYP2C9-inhibitor:	0.026
CYP2C9-substrate:	0.998
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.002
CYP3A4-inhibitor:	0.171
CYP3A4-substrate:	0.001

ADMET: Excretion

Clearance (CL):	1.334
Half-life (T1/2):	0.013

ADMET: Toxicity

hERG Blockers:	0.076
Human Hepatotoxicity (H-HT):	0.002
Drug-inuced Liver Injury (DILI):	0.0
AMES Toxicity:	0.003
Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.412
Skin Sensitization:	0.998
Carcinogencity:	0.21
Eye Corrosion:	0.689
Eye Irritation:	0.241
Respiratory Toxicity:	0.07

Download Data

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

Natural Product: NPC319517

Natural Product ID:	NPC319517
*Common Name:**	UYSHBKYVDAZLKJ-GMUISZSCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UYSHBKYVDAZLKJ-GMUISZSCSA-N
Standard InCHI:	InChI=1S/C73H134O17P2/c1-5-9-13-17-21-25-29-33-37-41-45-49-53-57-70(75)83-63-68(89-72(77)59-55-51-47-43-39-35-31-27-23-19-15-11-7-3)65-87-91(79,80)85-61-67(74)62-86-92(81,82)88-66-69(90-73(78)60-56-52-48-44-40-36-32-28-24-20-16-12-8-4)64-84-71(76)58-54-50-46-42-38-34-30-26-22-18-14-10-6-2/h25-32,67-69,74H,5-24,33-66H2,1-4H3,(H,79,80)(H,81,82)/t67?,68-,69-/m1/s1
SMILES:	CCCCCCC=CCCCCCCCC(=O)OCC(COP(=O)(O)OCC(COP(=O)(O)OCC(COC(=O)CCCCCCCC=CCCCCCC)OC(=O)CCCCCCCC=CCCCCCC)O)OC(=O)CCCCCCCC=CCCCCCC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	118987297
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000256] Glycerophospholipids [CHEMONTID:0003389] Glycerophosphoglycerophosphoglycerols [CHEMONTID:0001233] Cardiolipins

*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
NPO30193	Mycoplasma genitalium	Species	Mycoplasmataceae	Bacteria	n.a.	n.a.	n.a.	PMID[22817898]

☑ 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 NPC319517 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

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 NPC319517 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

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