NPASS Compound

Structure

NPC3853 OpenBabel06302216182D 85 94 0 0 1 0 0 0 0 0999 V2000 -9.3370 -5.0977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.2635 -5.3460 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.5118 -6.2725 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -11.4383 -6.5207 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -12.1165 -5.8425 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -11.8683 -4.9160 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.9418 -4.6677 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.5465 -4.2377 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.2982 -3.3112 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -11.3717 -3.0630 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.6935 -3.7412 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.7670 -3.4930 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.1235 -2.1365 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.8017 -1.4582 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -12.7282 -1.7065 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -12.9765 -2.6330 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -13.9030 -2.8813 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -13.4065 -1.0283 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.5535 -0.5317 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.2317 0.1465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.9835 1.0730 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -12.6617 1.7512 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -12.4135 2.6777 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -11.4870 2.9260 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -10.8087 2.2478 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -11.0570 1.3213 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.9557 2.7443 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.4592 4.5973 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6062 5.0938 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.1375 5.2755 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.9681 5.7551 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.9681 6.7143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.1375 7.1939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6579 8.0246 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.6170 8.0246 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3068 6.7143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3068 5.7551 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.4761 5.2755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6454 5.7551 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8147 5.2755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8147 4.3163 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.9841 3.8367 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.9841 4.7959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1534 4.3163 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3227 3.8367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3227 2.8776 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1534 2.3980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6330 1.5673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6738 1.5673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9841 2.8776 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.8147 2.3980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6454 2.8776 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6454 3.8367 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.3068 2.8776 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4761 4.3163 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.4761 3.3571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3068 3.8367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.1375 4.3163 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.9681 3.8367 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4920 2.3980 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4920 1.4388 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6614 0.9592 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6614 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4920 -0.4796 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3227 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3227 0.9592 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4920 -1.4388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8307 -0.4796 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8307 1.4388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9592 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8307 1.4388 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6614 0.9592 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6614 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8307 -0.4796 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8307 -1.4388 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 2.4920 -0.4796 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4920 1.4388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8307 2.3980 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.2387 3.8525 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -13.0917 3.3560 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -13.5882 1.5030 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -13.0430 -6.0907 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.6865 -7.4472 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.8335 -6.9507 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 85 1 6 0 0 0 4 5 1 0 0 0 0 4 84 1 1 0 0 0 5 6 1 0 0 0 0 5 83 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 6 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 16 1 0 0 0 0 10 11 1 6 0 0 0 10 13 1 0 0 0 0 11 12 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 19 1 6 0 0 0 15 16 1 0 0 0 0 15 18 1 1 0 0 0 16 17 1 6 0 0 0 19 20 1 0 0 0 0 21 20 1 6 0 0 0 21 22 1 0 0 0 0 21 26 1 0 0 0 0 22 23 1 0 0 0 0 22 82 1 1 0 0 0 23 24 1 0 0 0 0 23 81 1 6 0 0 0 24 25 1 0 0 0 0 24 80 1 1 0 0 0 25 26 1 0 0 0 0 25 27 1 6 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 30 28 1 6 0 0 0 30 37 1 0 0 0 0 30 58 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 32 33 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 36 1 1 0 0 0 37 38 1 0 0 0 0 38 55 1 0 0 0 0 38 39 2 0 0 0 0 39 40 1 0 0 0 0 41 40 1 6 0 0 0 41 42 1 0 0 0 0 41 53 1 0 0 0 0 42 50 1 0 0 0 0 42 43 1 6 0 0 0 42 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 46 60 1 6 0 0 0 47 48 1 0 0 0 0 47 49 1 0 0 0 0 47 50 1 0 0 0 0 50 51 1 6 0 0 0 51 52 1 0 0 0 0 52 53 1 0 0 0 0 53 54 1 6 0 0 0 53 55 1 0 0 0 0 55 56 1 1 0 0 0 55 57 1 0 0 0 0 57 58 1 0 0 0 0 58 59 1 1 0 0 0 61 60 1 1 0 0 0 61 62 1 0 0 0 0 61 66 1 0 0 0 0 62 63 1 0 0 0 0 62 69 1 6 0 0 0 63 64 1 0 0 0 0 63 68 1 1 0 0 0 64 65 1 0 0 0 0 64 67 1 1 0 0 0 65 66 1 0 0 0 0 70 69 1 1 0 0 0 70 71 1 0 0 0 0 70 76 1 0 0 0 0 71 72 1 0 0 0 0 71 79 1 6 0 0 0 72 73 1 0 0 0 0 72 78 1 6 0 0 0 73 74 1 0 0 0 0 73 77 1 1 0 0 0 74 75 1 6 0 0 0 74 76 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	1220.62
Volume:	1166.728
LogP:	2.153
LogD:	1.429
LogS:	-3.078
# Rotatable Bonds:	13
TPSA:	412.82
# H-Bond Aceptor:	26
# H-Bond Donor:	15
# Rings:	10
# Heavy Atoms:	26

MedChem Properties

QED Drug-Likeness Score:	0.054
Synthetic Accessibility Score:	7.267
Fsp3:	0.949
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:	-5.957
MDCK Permeability:	0.00031608197605237365
Pgp-inhibitor:	0.036
Pgp-substrate:	0.937
Human Intestinal Absorption (HIA):	0.987
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.057
Plasma Protein Binding (PPB):	60.804073333740234%
Volume Distribution (VD):	-0.209
Pgp-substrate:	19.918745040893555%

ADMET: Metabolism

CYP1A2-inhibitor:	0.0
CYP1A2-substrate:	0.067
CYP2C19-inhibitor:	0.001
CYP2C19-substrate:	0.072
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.003
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.044
CYP3A4-inhibitor:	0.034
CYP3A4-substrate:	0.001

ADMET: Excretion

Clearance (CL):	-0.285
Half-life (T1/2):	0.636

ADMET: Toxicity

hERG Blockers:	0.22
Human Hepatotoxicity (H-HT):	0.11
Drug-inuced Liver Injury (DILI):	0.02
AMES Toxicity:	0.093
Rat Oral Acute Toxicity:	0.138
Maximum Recommended Daily Dose:	0.969
Skin Sensitization:	0.278
Carcinogencity:	0.012
Eye Corrosion:	0.003
Eye Irritation:	0.008
Respiratory Toxicity:	0.907

Download Data

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

Natural Product: NPC3853

Natural Product ID:	NPC3853
*Common Name:**	PVNXMFDNBHBTQH-WZJLZQBYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PVNXMFDNBHBTQH-WZJLZQBYSA-N
Standard InCHI:	InChI=1S/C59H96O26/c1-23-34(63)38(67)42(71)49(78-23)83-46-28(20-60)80-48(45(74)41(46)70)77-22-29-37(66)40(69)44(73)51(81-29)85-53(75)59-17-16-54(3,4)18-26(59)25-10-11-31-56(7)14-13-33(55(5,6)30(56)12-15-57(31,8)58(25,9)19-32(59)62)82-52-47(36(65)27(61)21-76-52)84-50-43(72)39(68)35(64)24(2)79-50/h10,23-24,26-52,60-74H,11-22H2,1-9H3/t23-,24-,26-,27-,28+,29+,30-,31+,32+,33-,34-,35-,36-,37+,38+,39+,40-,41+,42+,43+,44+,45+,46+,47+,48+,49-,50-,51-,52-,56-,57+,58+,59+/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@@H](CO)O[C@H]([C@@H]([C@H]1O)O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)OC(=O)[C@]12CCC(C)(C)C[C@H]1C1=CC[C@@H]3[C@@]4(C)CC[C@@H](C(C)(C)[C@@H]4CC[C@@]3(C)[C@]1(C)C[C@H]2O)O[C@H]1[C@@H]([C@H]([C@H](CO1)O)O)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)O)O)O)O)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	21627942
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

*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
NPO22109	Streptomyces clavuligerus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[18450406]
NPO22109	Streptomyces clavuligerus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19941870]
NPO22554	Eunicea laciniata	Species	Plexauridae	Eukaryota	n.a.	Caribbean	n.a.	PMID[7769391]
NPO22494	Thalictrum rugosum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21909	Alkanna tinctoria	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22494	Thalictrum rugosum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22494	Thalictrum rugosum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22750	Resseliella theobaldi	Species	Cecidomyiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22494	Thalictrum rugosum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22109	Streptomyces clavuligerus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO27908	Bathynella natans	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO21909	Alkanna tinctoria	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO231	Phanera vahlii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22367	Strychnos hirsuta	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20517	Seseli elatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22554	Eunicea laciniata	Species	Plexauridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5093	Centaurea hermannii	Species	Asteraceae	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 NPC3853 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	268
0.1-0.2	1788
0.2-0.3	5149
0.3-0.4	11243
0.4-0.5	10860
0.5-0.6	6333
0.6-0.7	3937
0.7-0.8	1935
0.8-0.85	485
0.85-0.9	275
0.9-0.95	191
0.95-1	233

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 NPC3853 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	247
0.1-0.2	2108
0.2-0.3	3833
0.3-0.4	1919
0.4-0.5	614
0.5-0.6	268
0.6-0.7	126
0.7-0.8	31
0.8-0.85	1
0.85-0.9	1
0.9-0.95	2
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