NPASS Compound

Structure

NPC136637 OpenBabel06302215422D 63 63 0 0 1 0 0 0 0 0999 V2000 9.5263 -13.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -12.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -11.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -9.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -4.5000 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 3.4641 -3.0000 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 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 O 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 2.5981 -0.5000 0.0000 C 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 0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 1 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 O 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 0.0000 0.0000 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 -2.5981 -1.5000 0.0000 C 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 -3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 O 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 -2.0000 0.0000 O 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 -3.5000 0.0000 O 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 3.4641 1.0000 0.0000 O 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 1.7321 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 1.7321 3.0000 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 4.5000 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 0.0000 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 8.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 11.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 13.0000 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 1 0 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 20 19 1 6 0 0 0 20 21 1 0 0 0 0 20 46 1 0 0 0 0 21 22 1 0 0 0 0 23 22 1 1 0 0 0 23 24 1 0 0 0 0 23 33 1 0 0 0 0 24 25 1 0 0 0 0 24 42 1 6 0 0 0 25 26 1 0 0 0 0 25 38 1 1 0 0 0 26 27 1 0 0 0 0 26 34 1 1 0 0 0 27 28 1 1 0 0 0 27 33 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 32 1 0 0 0 0 34 35 1 0 0 0 0 35 36 2 0 0 0 0 35 37 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 42 43 1 0 0 0 0 43 44 2 0 0 0 0 43 45 1 0 0 0 0 46 47 1 0 0 0 0 47 48 2 0 0 0 0 47 49 1 0 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 55 56 1 0 0 0 0 56 57 2 0 0 0 0 57 58 1 0 0 0 0 58 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 M END $$$$

Physi-Chem Properties

Molecular Weight:	896.59
Volume:	952.111
LogP:	9.985
LogD:	4.701
LogS:	-2.959
# Rotatable Bonds:	44
TPSA:	176.26
# H-Bond Aceptor:	14
# H-Bond Donor:	0
# Rings:	1
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.025
Synthetic Accessibility Score:	4.731
Fsp3:	0.837
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:	-4.87
MDCK Permeability:	1.876694682323432e-06
Pgp-inhibitor:	0.694
Pgp-substrate:	0.578
Human Intestinal Absorption (HIA):	0.072
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.014
Plasma Protein Binding (PPB):	97.67717742919922%
Volume Distribution (VD):	2.199
Pgp-substrate:	4.318138599395752%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.035
CYP2C19-inhibitor:	0.123
CYP2C19-substrate:	0.038
CYP2C9-inhibitor:	0.039
CYP2C9-substrate:	0.07
CYP2D6-inhibitor:	0.992
CYP2D6-substrate:	0.005
CYP3A4-inhibitor:	0.789
CYP3A4-substrate:	0.151

ADMET: Excretion

Clearance (CL):	3.027
Half-life (T1/2):	0.502

ADMET: Toxicity

hERG Blockers:	0.303
Human Hepatotoxicity (H-HT):	0.894
Drug-inuced Liver Injury (DILI):	0.893
AMES Toxicity:	0.072
Rat Oral Acute Toxicity:	0.025
Maximum Recommended Daily Dose:	0.016
Skin Sensitization:	0.985
Carcinogencity:	0.061
Eye Corrosion:	0.024
Eye Irritation:	0.128
Respiratory Toxicity:	0.15

Download Data

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

Natural Product: NPC136637

Natural Product ID:	NPC136637
*Common Name:**	DIRZERNOENGADW-SPNCWQLDSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DIRZERNOENGADW-SPNCWQLDSA-N
Standard InCHI:	InChI=1S/C49H84O14/c1-7-9-11-13-15-17-19-21-23-25-27-29-31-33-44(54)57-35-42(62-45(55)34-32-30-28-26-24-22-20-18-16-14-12-10-8-2)36-58-49-48(61-41(6)53)47(60-40(5)52)46(59-39(4)51)43(63-49)37-56-38(3)50/h18,20,42-43,46-49H,7-17,19,21-37H2,1-6H3/b20-18-/t42-,43-,46+,47+,48-,49-/m1/s1
SMILES:	CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[C@H]1[C@@H]([C@H]([C@H]([C@@H](COC(=O)C)O1)OC(=O)C)OC(=O)C)OC(=O)C)OC(=O)CCCCCCC/C=CCCCCCC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000175] Glycerolipids [CHEMONTID:0000637] Glycosylglycerols [CHEMONTID:0003822] Glycosyldiradylglycerols [CHEMONTID:0003067] Glycosyldiacylglycerols

*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
NPO14060	Fischerella ambigua	Species	Hapalosiphonaceae	Bacteria	n.a.	n.a.	n.a.	PMID[15787461]
NPO12573	Hypericum annulatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17260692]
NPO14060	Fischerella ambigua	Species	Hapalosiphonaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19371071]
NPO420	Eucheuma muricatum	Species	Solieriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12573	Hypericum annulatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO420	Eucheuma muricatum	Species	Solieriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15556	Vernonia guineensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO420	Eucheuma muricatum	Species	Solieriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13801	Artemisia chamaemelifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14060	Fischerella ambigua	Species	Hapalosiphonaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO12573	Hypericum annulatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9797	Aconitum toxicum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17468	Hortia brasiliensis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15556	Vernonia guineensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14019	Paraphaeosphaeria sporulosa	Species	Didymosphaeriaceae	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 NPC136637 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	190
0.1-0.2	2155
0.2-0.3	7624
0.3-0.4	16048
0.4-0.5	9592
0.5-0.6	5721
0.6-0.7	1264
0.7-0.8	90
0.8-0.85	3
0.85-0.9	7
0.9-0.95	3
0.95-1	0

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 NPC136637 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	164
0.1-0.2	2808
0.2-0.3	3926
0.3-0.4	1512
0.4-0.5	529
0.5-0.6	188
0.6-0.7	23
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
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