NPASS Compound

Structure

NPC472544 OpenBabel07101719252D 27 29 0 0 1 0 0 0 0 0999 V2000 -4.6578 -3.0431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7421 -3.4448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3936 -2.3658 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7455 -3.5274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8695 -1.4864 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7761 -3.2819 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0341 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9389 -2.7350 0.0000 C 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 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8695 0.4864 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7455 2.5274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3247 -1.9458 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 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3936 1.3658 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7421 2.4448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7761 2.2819 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3247 0.9458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 2 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 -4.6578 2.0431 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.9389 1.7350 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 0 0 0 0 2 4 1 0 0 0 0 3 5 1 0 0 0 0 4 6 1 0 0 0 0 5 7 2 0 0 0 0 6 8 1 0 0 0 0 7 11 1 0 0 0 0 8 13 2 0 0 0 0 9 10 1 0 0 0 0 9 14 1 0 0 0 0 10 15 1 0 0 0 0 11 18 1 0 0 0 0 12 19 1 0 0 0 0 12 20 1 0 0 0 0 16 17 2 0 0 0 0 16 22 1 0 0 0 0 17 23 1 0 0 0 0 18 26 1 0 0 0 0 19 26 1 0 0 0 0 20 27 1 0 0 0 0 21 27 1 0 0 0 0 22 14 1 1 0 0 0 22 24 1 0 0 0 0 23 13 1 1 0 0 0 23 25 1 0 0 0 0 24 15 1 6 0 0 0 24 25 1 0 0 0 0 25 21 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	370.33
Volume:	429.371
LogP:	4.391
LogD:	4.189
LogS:	-2.874
# Rotatable Bonds:	0
TPSA:	24.06
# H-Bond Aceptor:	2
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.54
Synthetic Accessibility Score:	4.708
Fsp3:	0.76
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.236
MDCK Permeability:	1.6505528037669137e-06
Pgp-inhibitor:	0.001
Pgp-substrate:	0.036
Human Intestinal Absorption (HIA):	0.39
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.2
Plasma Protein Binding (PPB):	91.74307250976562%
Volume Distribution (VD):	0.629
Pgp-substrate:	2.794536590576172%

ADMET: Metabolism

CYP1A2-inhibitor:	0.127
CYP1A2-substrate:	0.207
CYP2C19-inhibitor:	0.093
CYP2C19-substrate:	0.862
CYP2C9-inhibitor:	0.015
CYP2C9-substrate:	0.041
CYP2D6-inhibitor:	0.985
CYP2D6-substrate:	0.9
CYP3A4-inhibitor:	0.849
CYP3A4-substrate:	0.281

ADMET: Excretion

Clearance (CL):	3.559
Half-life (T1/2):	0.62

ADMET: Toxicity

hERG Blockers:	0.158
Human Hepatotoxicity (H-HT):	0.84
Drug-inuced Liver Injury (DILI):	0.029
AMES Toxicity:	0.016
Rat Oral Acute Toxicity:	0.403
Maximum Recommended Daily Dose:	0.448
Skin Sensitization:	0.935
Carcinogencity:	0.005
Eye Corrosion:	0.006
Eye Irritation:	0.011
Respiratory Toxicity:	0.899

Download Data

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

Natural Product: NPC472544

Natural Product ID:	NPC472544
*Common Name:**	YMEPYIIXGBBSMO-XSGHGYHMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YMEPYIIXGBBSMO-XSGHGYHMSA-N
Standard InCHI:	InChI=1S/C25H42N2/c1-2-4-6-8-13-23-17-16-22-14-9-10-15-24(22)25(23)21-27-20-12-19-26-18-11-7-5-3-1/h5,7-8,13,16-17,22-27H,1-4,6,9-12,14-15,18-21H2/b7-5-,13-8+/t22-,23+,24+,25+/m0/s1
SMILES:	C1CCC=CCCNCCCNCC2C3CCCCC3C=CC2C=CCC1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3577064
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004707] Organic nitrogen compounds [CHEMONTID:0000278] Organonitrogen compounds [CHEMONTID:0002449] Amines [CHEMONTID:0002451] Secondary amines [CHEMONTID:0002228] Dialkylamines

*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
NPO33415	neopetrosia cf exigua	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[25585025]

☑ 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
GI50	3

Activity Type	# Activity
Cell Line	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT371	Cell Line	UO-31	Homo sapiens	GI50	>	20000.0	nM	PMID[473885]
NPT376	Cell Line	A498	Homo sapiens	GI50	>	20000.0	nM	PMID[473885]
NPT399	Cell Line	SF-295	Homo sapiens	GI50	>	20000.0	nM	PMID[473885]

☑ 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 NPC472544 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	283
0.1-0.2	9275
0.2-0.3	22968
0.3-0.4	8925
0.4-0.5	1040
0.5-0.6	162
0.6-0.7	34
0.7-0.8	8
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.8028	Intermediate Similarity	NPC174803
0.8028	Intermediate Similarity	NPC259989
0.7778	Intermediate Similarity	NPC231129
0.7656	Intermediate Similarity	NPC82919
0.7571	Intermediate Similarity	NPC472543
0.7368	Intermediate Similarity	NPC12035
0.7273	Intermediate Similarity	NPC329782
0.7273	Intermediate Similarity	NPC152039
0.7273	Intermediate Similarity	NPC474122
0.7273	Intermediate Similarity	NPC118329
0.7206	Intermediate Similarity	NPC476559
0.7179	Intermediate Similarity	NPC472312
0.7013	Intermediate Similarity	NPC211322
0.679	Remote Similarity	NPC471867
0.6757	Remote Similarity	NPC265789
0.6757	Remote Similarity	NPC21773
0.6707	Remote Similarity	NPC24733
0.6623	Remote Similarity	NPC7214
0.6579	Remote Similarity	NPC476904
0.6494	Remote Similarity	NPC125828
0.6341	Remote Similarity	NPC283277
0.6286	Remote Similarity	NPC311809
0.6271	Remote Similarity	NPC15231
0.625	Remote Similarity	NPC473959
0.6197	Remote Similarity	NPC219621
0.6173	Remote Similarity	NPC57599
0.6145	Remote Similarity	NPC215474
0.6136	Remote Similarity	NPC84171
0.6111	Remote Similarity	NPC145715
0.6094	Remote Similarity	NPC17518
0.6094	Remote Similarity	NPC106990
0.6087	Remote Similarity	NPC470369
0.6087	Remote Similarity	NPC470370
0.6071	Remote Similarity	NPC171639
0.6056	Remote Similarity	NPC317778
0.6049	Remote Similarity	NPC473446
0.6049	Remote Similarity	NPC473695
0.6	Remote Similarity	NPC58200
0.5957	Remote Similarity	NPC135799
0.5952	Remote Similarity	NPC471868
0.5938	Remote Similarity	NPC124851
0.5915	Remote Similarity	NPC472827
0.5914	Remote Similarity	NPC474164
0.5904	Remote Similarity	NPC476560
0.5882	Remote Similarity	NPC21667
0.5882	Remote Similarity	NPC161344
0.5873	Remote Similarity	NPC86683
0.5867	Remote Similarity	NPC37792
0.5857	Remote Similarity	NPC474415
0.5857	Remote Similarity	NPC173815
0.5857	Remote Similarity	NPC475696
0.5857	Remote Similarity	NPC474528
0.5846	Remote Similarity	NPC22765
0.5814	Remote Similarity	NPC57163
0.5814	Remote Similarity	NPC133162
0.5814	Remote Similarity	NPC116881
0.5795	Remote Similarity	NPC43308
0.5775	Remote Similarity	NPC324944
0.5775	Remote Similarity	NPC472830
0.5763	Remote Similarity	NPC473035
0.5763	Remote Similarity	NPC326791
0.5761	Remote Similarity	NPC476754
0.5733	Remote Similarity	NPC469970
0.5732	Remote Similarity	NPC308050
0.5729	Remote Similarity	NPC34193
0.5729	Remote Similarity	NPC118275
0.5714	Remote Similarity	NPC202189
0.5699	Remote Similarity	NPC329430
0.5696	Remote Similarity	NPC476329
0.5694	Remote Similarity	NPC475716
0.5694	Remote Similarity	NPC474420
0.5694	Remote Similarity	NPC474455
0.5694	Remote Similarity	NPC474454
0.5682	Remote Similarity	NPC157479
0.5682	Remote Similarity	NPC258046
0.5682	Remote Similarity	NPC166458
0.567	Remote Similarity	NPC176012
0.5652	Remote Similarity	NPC476753
0.5652	Remote Similarity	NPC476752
0.5645	Remote Similarity	NPC177470
0.5641	Remote Similarity	NPC138409
0.5641	Remote Similarity	NPC184919
0.5634	Remote Similarity	NPC474457
0.5632	Remote Similarity	NPC169016
0.561	Remote Similarity	NPC476308
0.561	Remote Similarity	NPC139658
0.5606	Remote Similarity	NPC17810
0.56	Remote Similarity	NPC53276

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 NPC472544 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	188
0.1-0.2	1300
0.2-0.3	4870
0.3-0.4	2371
0.4-0.5	353
0.5-0.6	66
0.6-0.7	2
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
0.7465	Intermediate Similarity	NPD5365	Phase 2
0.6562	Remote Similarity	NPD3722	Approved
0.6562	Remote Similarity	NPD3721	Approved
0.6163	Remote Similarity	NPD4146	Approved
0.6163	Remote Similarity	NPD3426	Approved
0.6163	Remote Similarity	NPD3428	Approved
0.6163	Remote Similarity	NPD4145	Approved
0.5977	Remote Similarity	NPD2002	Discontinued
0.5968	Remote Similarity	NPD9674	Approved
0.5968	Remote Similarity	NPD9675	Approved
0.5955	Remote Similarity	NPD5915	Approved
0.5902	Remote Similarity	NPD390	Approved
0.5902	Remote Similarity	NPD718	Approved
0.5814	Remote Similarity	NPD3429	Approved
0.5814	Remote Similarity	NPD3427	Approved
0.5761	Remote Similarity	NPD3982	Approved
0.5761	Remote Similarity	NPD3980	Approved
0.5758	Remote Similarity	NPD4834	Discontinued
0.5714	Remote Similarity	NPD4543	Discontinued
0.5699	Remote Similarity	NPD5554	Approved
0.5652	Remote Similarity	NPD3727	Discontinued
0.5638	Remote Similarity	NPD2005	Discontinued
0.5632	Remote Similarity	NPD785	Approved
0.5606	Remote Similarity	NPD8262	Approved

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