NPASS Compound

Structure

NPC185668 OpenBabel06302215322D 44 53 0 0 1 0 0 0 0 0999 V2000 9.8730 1.2400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1399 1.9083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3521 2.8773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1947 1.6073 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.4603 2.2763 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.5152 1.9749 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.3032 1.0059 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.0375 0.3370 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.8251 -0.6325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8796 -0.9343 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1452 -0.2654 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.4117 0.4028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1997 -0.5671 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.8685 -1.1764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4657 0.1014 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.6782 1.0709 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6237 1.3727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3577 0.7041 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.0916 0.0356 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5202 -0.2003 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3086 -1.1689 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4460 -1.6604 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6468 -2.6326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0037 -2.8703 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4168 -2.5157 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3282 -1.8359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1516 -1.6401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2977 -1.1429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3096 -0.9764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.7187 0.0000 C 0 0 1 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 0.7187 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3146 0.3967 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6032 1.3808 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6067 1.1387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0261 0.3176 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5172 -0.6869 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8044 -1.3427 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5425 -0.6674 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6335 -2.7421 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.0425 -1.8375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9826 0.6383 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5700 1.6741 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6534 3.1601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 4 2 1 1 0 0 0 4 5 1 0 0 0 0 4 42 1 0 0 0 0 5 6 1 0 0 0 0 5 44 1 1 0 0 0 6 7 1 0 0 0 0 6 43 1 6 0 0 0 7 18 1 0 0 0 0 7 8 1 0 0 0 0 7 43 1 6 0 0 0 8 9 1 1 0 0 0 8 42 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 18 1 0 0 0 0 11 12 1 1 0 0 0 11 13 1 0 0 0 0 13 41 1 0 0 0 0 13 14 1 6 0 0 0 13 15 1 0 0 0 0 15 16 1 6 0 0 0 15 20 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 6 0 0 0 20 21 1 1 0 0 0 20 36 1 0 0 0 0 21 41 2 0 0 0 0 21 22 1 0 0 0 0 22 38 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 40 1 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 38 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 28 30 1 0 0 0 0 30 31 1 1 0 0 0 30 37 1 0 0 0 0 32 31 1 6 0 0 0 32 33 1 0 0 0 0 32 37 1 0 0 0 0 33 34 1 0 0 0 0 33 35 1 0 0 0 0 33 36 1 0 0 0 0 37 38 1 0 0 0 0 37 39 1 6 0 0 0 40 41 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	599.32
Volume:	610.863
LogP:	5.344
LogD:	3.649
LogS:	-5.665
# Rotatable Bonds:	1
TPSA:	107.47
# H-Bond Aceptor:	7
# H-Bond Donor:	4
# Rings:	10
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.271
Synthetic Accessibility Score:	6.555
Fsp3:	0.676
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:	-5.386
MDCK Permeability:	9.038149073603563e-06
Pgp-inhibitor:	0.977
Pgp-substrate:	0.994
Human Intestinal Absorption (HIA):	0.037
20% Bioavailability (F20%):	0.804
30% Bioavailability (F30%):	0.928

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.954
Plasma Protein Binding (PPB):	85.14493560791016%
Volume Distribution (VD):	2.113
Pgp-substrate:	6.764741897583008%

ADMET: Metabolism

CYP1A2-inhibitor:	0.022
CYP1A2-substrate:	0.967
CYP2C19-inhibitor:	0.07
CYP2C19-substrate:	0.626
CYP2C9-inhibitor:	0.181
CYP2C9-substrate:	0.062
CYP2D6-inhibitor:	0.029
CYP2D6-substrate:	0.645
CYP3A4-inhibitor:	0.657
CYP3A4-substrate:	0.876

ADMET: Excretion

Clearance (CL):	5.749
Half-life (T1/2):	0.071

ADMET: Toxicity

hERG Blockers:	0.931
Human Hepatotoxicity (H-HT):	0.797
Drug-inuced Liver Injury (DILI):	0.355
AMES Toxicity:	0.025
Rat Oral Acute Toxicity:	0.985
Maximum Recommended Daily Dose:	0.99
Skin Sensitization:	0.198
Carcinogencity:	0.93
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.988

Download Data

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

Natural Product: NPC185668

Natural Product ID:	NPC185668
*Common Name:**	LTCFBVUSILPMGG-BRSLXYMHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	LTCFBVUSILPMGG-BRSLXYMHSA-N
Standard InCHI:	InChI=1S/C37H45NO6/c1-16(2)28-27(39)31-37(44-31)23(42-28)11-12-33(6)34(7)19(10-13-35(33,37)40)29-25-24-21(38-30(25)34)9-8-18-14-17(3)20-15-22(32(4,5)43-29)36(20,41)26(18)24/h8-9,19-20,22-23,27-29,31,38-41H,1,3,10-15H2,2,4-7H3/t19-,20+,22+,23-,27-,28+,29-,31+,33+,34+,35-,36+,37-/m0/s1
SMILES:	C=C(C)[C@@H]1[C@@H]([C@@H]2[C@]3([C@H](CC[C@]4(C)[C@]5(C)[C@@H](CC[C@@]34O)[C@H]3c4c6c(ccc7CC(=C)[C@H]8C[C@H](C(C)(C)O3)[C@]8(c67)O)[nH]c54)O1)O2)O
Synthetic Gene Cluster:	BGC0001375;
ChEMBL Identifier:	n.a.
PubChem CID:	3086087
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001640] Naphthopyrans

*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
NPO40568	Mucor irregularis QEN-189	Strain	Mucoraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27462726]

☑ 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	5
Others	57

Activity Type	# Activity
Cell Line	49
NON-MOLECULAR	13

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT83	Cell Line	MCF7	Homo sapiens	GI	=	100.41	%	PMID[24273638]
NPT308	Cell Line	CAKI-1	Homo sapiens	GI	=	106.87	%	PMID[24273638]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	=	20300.0	nM	PMID[24273638]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	=	25400.0	nM	PMID[24273638]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	17500.0	nM	PMID[24273638]
NPT784	Cell Line	MDA-MB-468	Homo sapiens	GI	=	96.61	%	PMID[24273638]
NPT396	Cell Line	T47D	Homo sapiens	GI	=	94.75	%	PMID[24273638]
NPT457	Cell Line	BT-549	Homo sapiens	GI	=	100.62	%	PMID[24273638]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	GI	=	101.18	%	PMID[24273638]
NPT90	Cell Line	DU-145	Homo sapiens	GI	=	100.05	%	PMID[24273638]
NPT306	Cell Line	PC-3	Homo sapiens	GI	=	82.89	%	PMID[24273638]
NPT384	Cell Line	TK-10	Homo sapiens	GI	=	107.43	%	PMID[24273638]
NPT368	Cell Line	SN12C	Homo sapiens	GI	=	99.19	%	PMID[24273638]
NPT406	Cell Line	RXF 393	Homo sapiens	GI	=	94.95	%	PMID[24273638]
NPT369	Cell Line	ACHN	Homo sapiens	GI	=	101.41	%	PMID[24273638]
NPT401	Cell Line	786-0	Homo sapiens	GI	=	96.21	%	PMID[24273638]
NPT146	Cell Line	SK-OV-3	Homo sapiens	GI	=	102.81	%	PMID[24273638]
NPT458	Cell Line	IGROV-1	Homo sapiens	GI	=	89.66	%	PMID[24273638]
NPT373	Cell Line	SK-MEL-5	Homo sapiens	GI	=	103.52	%	PMID[24273638]
NPT170	Cell Line	SK-MEL-28	Homo sapiens	GI	=	109.62	%	PMID[24273638]
NPT147	Cell Line	SK-MEL-2	Homo sapiens	GI	=	96.38	%	PMID[24273638]
NPT400	Cell Line	MDA-MB-435	Homo sapiens	GI	=	106.43	%	PMID[24273638]
NPT387	Cell Line	M14	Homo sapiens	GI	=	100.37	%	PMID[24273638]
NPT375	Cell Line	Malme-3M	Homo sapiens	GI	=	98.53	%	PMID[24273638]
NPT390	Cell Line	LOX IMVI	Homo sapiens	GI	=	104.83	%	PMID[24273638]
NPT380	Cell Line	U-251	Homo sapiens	GI	=	98.98	%	PMID[24273638]
NPT392	Cell Line	SNB-75	Homo sapiens	GI	=	84.36	%	PMID[24273638]
NPT383	Cell Line	SNB-19	Homo sapiens	GI	=	100.59	%	PMID[24273638]
NPT374	Cell Line	SF-539	Homo sapiens	GI	=	90.7	%	PMID[24273638]
NPT395	Cell Line	SF-268	Homo sapiens	GI	=	88.93	%	PMID[24273638]
NPT323	Cell Line	SW-620	Homo sapiens	GI	=	106.14	%	PMID[24273638]
NPT386	Cell Line	KM12	Homo sapiens	GI	=	109.93	%	PMID[24273638]
NPT139	Cell Line	HT-29	Homo sapiens	GI	=	90.56	%	PMID[24273638]
NPT393	Cell Line	HCT-116	Homo sapiens	GI	=	92.44	%	PMID[24273638]
NPT391	Cell Line	HCC 2998	Homo sapiens	GI	=	103.8	%	PMID[24273638]
NPT407	Cell Line	COLO 205	Homo sapiens	GI	=	105.66	%	PMID[24273638]
NPT455	Cell Line	NCI-H522	Homo sapiens	GI	=	86.01	%	PMID[24273638]
NPT397	Cell Line	NCI-H460	Homo sapiens	GI	=	100.5	%	PMID[24273638]
NPT388	Cell Line	NCI-H322M	Homo sapiens	GI	=	99.41	%	PMID[24273638]
NPT370	Cell Line	NCI-H23	Homo sapiens	GI	=	117.08	%	PMID[24273638]
NPT405	Cell Line	NCI-H226	Homo sapiens	GI	=	98.2	%	PMID[24273638]
NPT379	Cell Line	HOP-62	Homo sapiens	GI	=	99.24	%	PMID[24273638]
NPT81	Cell Line	A549	Homo sapiens	GI	=	92.64	%	PMID[24273638]
NPT385	Cell Line	SR	Homo sapiens	GI	=	91.94	%	PMID[24273638]
NPT389	Cell Line	RPMI-8226	Homo sapiens	GI	=	72.48	%	PMID[24273638]
NPT112	Cell Line	MOLT-4	Homo sapiens	GI	=	78.0	%	PMID[24273638]
NPT111	Cell Line	K562	Homo sapiens	GI	=	76.91	%	PMID[24273638]
NPT116	Cell Line	HL-60	Homo sapiens	GI	=	100.62	%	PMID[24273638]
NPT404	Cell Line	CCRF-CEM	Homo sapiens	GI	=	67.99	%	PMID[24273638]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI	=	92.23	%	PMID[24273638]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI	=	72.46	%	PMID[24273638]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI	=	108.79	%	PMID[24273638]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI	=	96.88	%	PMID[24273638]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI	=	115.49	%	PMID[24273638]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI	=	108.77	%	PMID[24273638]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI	=	111.36	%	PMID[24273638]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI	=	100.98	%	PMID[24273638]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI	=	97.07	%	PMID[24273638]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI	=	98.87	%	PMID[24273638]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI	=	104.16	%	PMID[24273638]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	10000.0	nM	PMID[27462726]

☑ 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 NPC185668 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	574
0.1-0.2	1943
0.2-0.3	6416
0.3-0.4	17666
0.4-0.5	11781
0.5-0.6	3225
0.6-0.7	969
0.7-0.8	90
0.8-0.85	12
0.85-0.9	11
0.9-0.95	7
0.95-1	3

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 NPC185668 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	330
0.1-0.2	591
0.2-0.3	813
0.3-0.4	2648
0.4-0.5	3283
0.5-0.6	1271
0.6-0.7	210
0.7-0.8	4
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