NPASS Compound

Structure

CID115959 OpenBabel06191715472D 30 29 0 0 0 0 0 0 0 0999 V2000 12.9904 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 3.0000 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 6.0622 -0.5000 0.0000 C 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 11.2583 2.5000 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 8.6603 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 12.1244 3.0000 0.0000 C 0 0 0 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 6.9282 -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 0 0 0 0 0 0 0 0 0 0 10.3923 3.0000 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 7.7942 1.5000 0.0000 C 0 0 0 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 9.5263 1.5000 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 12.9904 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 2.5000 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 1 25 1 0 0 0 0 2 25 1 0 0 0 0 3 26 1 0 0 0 0 4 26 1 0 0 0 0 5 27 1 0 0 0 0 6 28 1 0 0 0 0 7 29 1 0 0 0 0 8 30 1 0 0 0 0 9 10 1 0 0 0 0 9 17 1 0 0 0 0 10 18 1 0 0 0 0 11 15 1 0 0 0 0 11 19 1 0 0 0 0 12 16 1 0 0 0 0 12 20 1 0 0 0 0 13 21 1 0 0 0 0 13 23 1 0 0 0 0 14 22 1 0 0 0 0 14 24 1 0 0 0 0 15 25 2 0 0 0 0 16 26 2 0 0 0 0 17 27 2 3 0 0 0 18 28 2 3 0 0 0 19 29 1 0 0 0 0 20 30 1 0 0 0 0 21 27 1 0 0 0 0 22 28 1 0 0 0 0 23 29 2 3 0 0 0 24 30 2 3 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	410.39
Volume:	511.617
LogP:	12.248
LogD:	6.663
LogS:	-7.149
# Rotatable Bonds:	15
TPSA:	0.0
# H-Bond Aceptor:	0
# H-Bond Donor:	0
# Rings:	0
# Heavy Atoms:	0

MedChem Properties

QED Drug-Likeness Score:	0.186
Synthetic Accessibility Score:	2.804
Fsp3:	0.6
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:	-4.705
MDCK Permeability:	8.867527867550962e-06
Pgp-inhibitor:	0.03
Pgp-substrate:	0.012
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.999
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.019
Plasma Protein Binding (PPB):	86.4839859008789%
Volume Distribution (VD):	12.026
Pgp-substrate:	4.236446857452393%

ADMET: Metabolism

CYP1A2-inhibitor:	0.354
CYP1A2-substrate:	0.11
CYP2C19-inhibitor:	0.237
CYP2C19-substrate:	0.074
CYP2C9-inhibitor:	0.599
CYP2C9-substrate:	0.956
CYP2D6-inhibitor:	0.021
CYP2D6-substrate:	0.025
CYP3A4-inhibitor:	0.561
CYP3A4-substrate:	0.109

ADMET: Excretion

Clearance (CL):	13.462
Half-life (T1/2):	0.005

ADMET: Toxicity

hERG Blockers:	0.183
Human Hepatotoxicity (H-HT):	0.982
Drug-inuced Liver Injury (DILI):	0.02
AMES Toxicity:	0.0
Rat Oral Acute Toxicity:	0.002
Maximum Recommended Daily Dose:	0.033
Skin Sensitization:	0.979
Carcinogencity:	0.131
Eye Corrosion:	0.01
Eye Irritation:	0.766
Respiratory Toxicity:	0.001

Download Data

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

Natural Product: NPC115959

Natural Product ID:	NPC115959
*Common Name:**	2,6,10,15,19,23-Hexamethyltetracosa-2,6,10,14,18,22-Hexaene
IUPAC Name:	2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene
Synonyms:
Standard InCHIKey:	YYGNTYWPHWGJRM-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C30H50/c1-25(2)15-11-19-29(7)23-13-21-27(5)17-9-10-18-28(6)22-14-24-30(8)20-12-16-26(3)4/h15-18,23-24H,9-14,19-22H2,1-8H3
SMILES:	CC(=CCCC=C(CCC=C(CCC=C(C)C)C)C)CCC=C(CCC=C(C)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3561564
PubChem CID:	1105
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
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[10579867]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	subterranean part	n.a.	n.a.	PMID[11374949]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[11536386]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[11975496]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[24035341]
NPO14556	Iris missouriensis	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3655793]
NPO14556	Iris missouriensis	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3734815]
NPO16297	Gentiana arisanensis	Species	Gentianaceae	Eukaryota	Whole Plant	Yu Shieh, Chiayi Hsieh, Taiwan	1994-APR	PMID[9287421]
NPO12948	Solanum dulcamara	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12948	Solanum dulcamara	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12948	Solanum dulcamara	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14556	Iris missouriensis	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14977	Harrisina brillians	Species	Zygaenidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16297	Gentiana arisanensis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15721	Derris reticulata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7086	Parantica melaneus	Species	Nymphalidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14782	Scymnorhinus lichi	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO13675	Sphaceloma randii	Species	Elsinoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16918	Ballota lanata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18413	Eucalyptus ovata	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15555	Sesbania madagascariensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12948	Solanum dulcamara	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22020	Ochrolechia pallescens	Species	Ochrolechiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15637	Polygala cyparissias	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	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

Activity Type	# Activity
IC50	10

Activity Type	# Activity
Others	10

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		IC50	n.a.	20000.0	nM	PMID[466621]
NPT2	Others	Unspecified		IC50	n.a.	10000.0	nM	PMID[466621]

☑ 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 NPC115959 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	1368
0.1-0.2	27021
0.2-0.3	10978
0.3-0.4	2477
0.4-0.5	592
0.5-0.6	186
0.6-0.7	47
0.7-0.8	14
0.8-0.85	6
0.85-0.9	5
0.9-0.95	1
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC123965
0.931	High Similarity	NPC471327
0.8929	High Similarity	NPC138325
0.871	High Similarity	NPC305759
0.871	High Similarity	NPC173592
0.871	High Similarity	NPC99088
0.8621	High Similarity	NPC34671
0.8621	High Similarity	NPC138113
0.8333	Intermediate Similarity	NPC60288
0.8182	Intermediate Similarity	NPC92224
0.8065	Intermediate Similarity	NPC3649
0.8065	Intermediate Similarity	NPC151719
0.8065	Intermediate Similarity	NPC66577
0.8065	Intermediate Similarity	NPC100879
0.8065	Intermediate Similarity	NPC206088
0.7812	Intermediate Similarity	NPC213749
0.7714	Intermediate Similarity	NPC266298
0.7667	Intermediate Similarity	NPC64176
0.7667	Intermediate Similarity	NPC288991
0.7667	Intermediate Similarity	NPC262789
0.7353	Intermediate Similarity	NPC182392
0.7273	Intermediate Similarity	NPC13217
0.7222	Intermediate Similarity	NPC180840
0.7143	Intermediate Similarity	NPC282119
0.7105	Intermediate Similarity	NPC269823
0.7097	Intermediate Similarity	NPC179103
0.7097	Intermediate Similarity	NPC76765
0.697	Remote Similarity	NPC196831
0.6944	Remote Similarity	NPC190810
0.6944	Remote Similarity	NPC34764
0.6944	Remote Similarity	NPC76145
0.6944	Remote Similarity	NPC185839
0.6923	Remote Similarity	NPC256766
0.6923	Remote Similarity	NPC213538
0.6774	Remote Similarity	NPC10183
0.6757	Remote Similarity	NPC45727
0.6757	Remote Similarity	NPC139717
0.6757	Remote Similarity	NPC229262
0.6757	Remote Similarity	NPC239039
0.6757	Remote Similarity	NPC48638
0.6757	Remote Similarity	NPC297643
0.675	Remote Similarity	NPC116934
0.6667	Remote Similarity	NPC88325
0.6667	Remote Similarity	NPC38497
0.6585	Remote Similarity	NPC138935
0.6579	Remote Similarity	NPC182840
0.6579	Remote Similarity	NPC103213
0.6579	Remote Similarity	NPC29091
0.6579	Remote Similarity	NPC255042
0.6571	Remote Similarity	NPC62779
0.6486	Remote Similarity	NPC201753
0.6452	Remote Similarity	NPC266144
0.6452	Remote Similarity	NPC287191
0.6452	Remote Similarity	NPC31891
0.6452	Remote Similarity	NPC266539
0.6429	Remote Similarity	NPC140501
0.6429	Remote Similarity	NPC160628
0.6429	Remote Similarity	NPC49088
0.6429	Remote Similarity	NPC178306
0.641	Remote Similarity	NPC12319
0.641	Remote Similarity	NPC18205
0.641	Remote Similarity	NPC183670
0.6279	Remote Similarity	NPC308331
0.6279	Remote Similarity	NPC323445
0.625	Remote Similarity	NPC218918
0.625	Remote Similarity	NPC469969
0.625	Remote Similarity	NPC188596
0.625	Remote Similarity	NPC144023
0.625	Remote Similarity	NPC120926
0.6207	Remote Similarity	NPC96619
0.619	Remote Similarity	NPC477686
0.6136	Remote Similarity	NPC124851
0.6136	Remote Similarity	NPC318549
0.6129	Remote Similarity	NPC38513
0.6111	Remote Similarity	NPC12889
0.6098	Remote Similarity	NPC473912
0.6098	Remote Similarity	NPC177470
0.6098	Remote Similarity	NPC194586
0.6098	Remote Similarity	NPC67761
0.6098	Remote Similarity	NPC88079
0.6098	Remote Similarity	NPC68889
0.6098	Remote Similarity	NPC209279
0.6098	Remote Similarity	NPC51758
0.6098	Remote Similarity	NPC180871
0.6098	Remote Similarity	NPC108494
0.6071	Remote Similarity	NPC225855
0.6047	Remote Similarity	NPC191337
0.6	Remote Similarity	NPC17518
0.6	Remote Similarity	NPC22765
0.6	Remote Similarity	NPC17810
0.6	Remote Similarity	NPC56917
0.5952	Remote Similarity	NPC106819
0.5952	Remote Similarity	NPC86538
0.5952	Remote Similarity	NPC109813
0.5952	Remote Similarity	NPC301972
0.5952	Remote Similarity	NPC216921
0.5952	Remote Similarity	NPC60556
0.5909	Remote Similarity	NPC262558
0.5909	Remote Similarity	NPC197467
0.5909	Remote Similarity	NPC8610
0.5909	Remote Similarity	NPC128280
0.5897	Remote Similarity	NPC92863
0.5897	Remote Similarity	NPC40434
0.5897	Remote Similarity	NPC155880
0.5897	Remote Similarity	NPC34873
0.587	Remote Similarity	NPC329773
0.587	Remote Similarity	NPC474460
0.587	Remote Similarity	NPC182102
0.587	Remote Similarity	NPC26960
0.5854	Remote Similarity	NPC259702
0.5833	Remote Similarity	NPC266979
0.5814	Remote Similarity	NPC6963
0.5814	Remote Similarity	NPC304079
0.5814	Remote Similarity	NPC12907
0.5814	Remote Similarity	NPC202189
0.5814	Remote Similarity	NPC248411
0.575	Remote Similarity	NPC217923
0.575	Remote Similarity	NPC101811
0.575	Remote Similarity	NPC15934
0.5745	Remote Similarity	NPC473672
0.5745	Remote Similarity	NPC234829
0.5745	Remote Similarity	NPC474495
0.5714	Remote Similarity	NPC33192
0.5682	Remote Similarity	NPC165651
0.5682	Remote Similarity	NPC13991
0.5682	Remote Similarity	NPC270706
0.5682	Remote Similarity	NPC221379
0.5682	Remote Similarity	NPC241784
0.5682	Remote Similarity	NPC296337
0.5682	Remote Similarity	NPC76976
0.5682	Remote Similarity	NPC24824
0.5682	Remote Similarity	NPC26600
0.5682	Remote Similarity	NPC47946
0.5682	Remote Similarity	NPC114239
0.5682	Remote Similarity	NPC86683
0.5682	Remote Similarity	NPC210560
0.5652	Remote Similarity	NPC267110
0.5625	Remote Similarity	NPC208638
0.561	Remote Similarity	NPC329762
0.561	Remote Similarity	NPC27444
0.561	Remote Similarity	NPC103236
0.561	Remote Similarity	NPC111474
0.561	Remote Similarity	NPC101147

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 NPC115959 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	953
0.1-0.2	6977
0.2-0.3	1058
0.3-0.4	121
0.4-0.5	26
0.5-0.6	11
0.6-0.7	2
0.7-0.8	2
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
0.75	Intermediate Similarity	NPD5783	Phase 3
0.6944	Remote Similarity	NPD319	Phase 1
0.6429	Remote Similarity	NPD4265	Approved
0.641	Remote Similarity	NPD1153	Clinical (unspecified phase)
0.6	Remote Similarity	NPD8262	Approved
0.5814	Remote Similarity	NPD9674	Approved
0.5814	Remote Similarity	NPD9675	Approved
0.5745	Remote Similarity	NPD6927	Phase 3
0.5682	Remote Similarity	NPD39	Approved
0.5652	Remote Similarity	NPD4220	Pre-registration

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