NPASS Compound

Structure

NPC207281 OpenBabel06302215222D 88 96 0 0 1 0 0 0 0 0999 V2000 5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -4.0000 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 3.4641 -4.0000 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 4.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -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 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 3 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 0.0000 -1.0000 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 -1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 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 -0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 C 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 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 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 O 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 3.4641 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3301 3.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1962 3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.1962 2.0000 0.0000 C 0 0 1 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 6.0622 0.5000 0.0000 O 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 7.7942 0.5000 0.0000 O 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 7.7942 -1.5000 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 9.5263 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 0.5000 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 6.0622 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 3.5000 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 -0.0000 5.0000 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 0.8660 6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 8.0000 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 -0.0000 8.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 8.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 7.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.1962 8.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.0622 7.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.0622 6.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.1962 6.0000 0.0000 C 0 0 1 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 6.0622 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 6.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 8.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 9.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 5.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 4.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 5.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 6.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 6.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 8.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 6.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 3.5000 0.0000 O 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 -2.5981 0.5000 0.0000 O 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 -0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 88 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 3 0 0 0 8 9 1 0 0 0 0 9 10 2 3 0 0 0 9 87 1 0 0 0 0 10 11 1 0 0 0 0 12 11 1 6 0 0 0 12 13 1 0 0 0 0 12 83 1 0 0 0 0 13 14 1 0 0 0 0 13 86 1 1 0 0 0 14 15 1 0 0 0 0 14 85 1 6 0 0 0 15 16 1 0 0 0 0 15 84 1 1 0 0 0 16 17 1 6 0 0 0 16 83 1 0 0 0 0 17 18 1 0 0 0 0 18 23 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 20 48 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 22 25 1 0 0 0 0 23 24 1 0 0 0 0 26 25 1 1 0 0 0 26 27 1 0 0 0 0 26 44 1 0 0 0 0 27 28 1 0 0 0 0 27 47 1 6 0 0 0 28 29 1 0 0 0 0 28 46 1 1 0 0 0 29 30 1 0 0 0 0 29 45 1 6 0 0 0 30 31 1 1 0 0 0 30 44 1 0 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 35 36 2 3 0 0 0 36 37 1 0 0 0 0 37 42 2 0 0 0 0 37 38 1 0 0 0 0 38 39 2 0 0 0 0 39 40 1 0 0 0 0 40 41 2 0 0 0 0 40 43 1 0 0 0 0 41 42 1 0 0 0 0 48 70 1 0 0 0 0 48 49 2 0 0 0 0 49 50 1 0 0 0 0 49 71 1 0 0 0 0 50 51 2 0 0 0 0 51 56 1 0 0 0 0 51 52 1 0 0 0 0 52 53 2 0 0 0 0 52 70 1 0 0 0 0 53 54 1 0 0 0 0 54 55 2 0 0 0 0 54 58 1 0 0 0 0 55 56 1 0 0 0 0 56 57 2 0 0 0 0 59 58 1 1 0 0 0 59 60 1 0 0 0 0 59 66 1 0 0 0 0 60 61 1 0 0 0 0 60 69 1 6 0 0 0 61 62 1 0 0 0 0 61 68 1 1 0 0 0 62 63 1 0 0 0 0 62 67 1 6 0 0 0 63 64 1 1 0 0 0 63 66 1 0 0 0 0 64 65 1 0 0 0 0 72 71 1 1 0 0 0 72 73 1 0 0 0 0 72 79 1 0 0 0 0 73 74 1 0 0 0 0 73 82 1 6 0 0 0 74 75 1 0 0 0 0 74 81 1 1 0 0 0 75 76 1 0 0 0 0 75 80 1 6 0 0 0 76 77 1 1 0 0 0 76 79 1 0 0 0 0 77 78 1 0 0 0 0 M CHG 1 10 1 M END $$$$

Physi-Chem Properties

Molecular Weight:	1243.33
Volume:	1143.778
LogP:	0.193
LogD:	-0.165
LogS:	-3.104
# Rotatable Bonds:	21
TPSA:	504.89
# H-Bond Aceptor:	31
# H-Bond Donor:	18
# Rings:	9
# Heavy Atoms:	31

MedChem Properties

QED Drug-Likeness Score:	0.021
Synthetic Accessibility Score:	6.858
Fsp3:	0.421
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.919
MDCK Permeability:	0.00010035835293820128
Pgp-inhibitor:	0.0
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.992
20% Bioavailability (F20%):	0.345
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.19
Plasma Protein Binding (PPB):	86.04161834716797%
Volume Distribution (VD):	0.296
Pgp-substrate:	19.132877349853516%

ADMET: Metabolism

CYP1A2-inhibitor:	0.076
CYP1A2-substrate:	0.001
CYP2C19-inhibitor:	0.017
CYP2C19-substrate:	0.041
CYP2C9-inhibitor:	0.004
CYP2C9-substrate:	0.054
CYP2D6-inhibitor:	0.036
CYP2D6-substrate:	0.091
CYP3A4-inhibitor:	0.021
CYP3A4-substrate:	0.001

ADMET: Excretion

Clearance (CL):	0.473
Half-life (T1/2):	0.603

ADMET: Toxicity

hERG Blockers:	0.26
Human Hepatotoxicity (H-HT):	0.195
Drug-inuced Liver Injury (DILI):	0.971
AMES Toxicity:	0.106
Rat Oral Acute Toxicity:	0.017
Maximum Recommended Daily Dose:	0.001
Skin Sensitization:	0.929
Carcinogencity:	0.058
Eye Corrosion:	0.003
Eye Irritation:	0.009
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: NPC207281

Natural Product ID:	NPC207281
*Common Name:**	RRFVMPFCZKNXKT-LHKMMSPXSA-O
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RRFVMPFCZKNXKT-LHKMMSPXSA-O
Standard InCHI:	InChI=1S/C57H62O31/c58-18-34-41(66)45(70)49(74)54(85-34)80-27-15-29(62)28-17-33(84-57-50(75)46(71)42(67)35(19-59)86-57)53(81-30(28)16-27)24-13-31(82-55-51(76)47(72)43(68)36(87-55)20-78-38(63)11-5-22-1-7-25(60)8-2-22)40(65)32(14-24)83-56-52(77)48(73)44(69)37(88-56)21-79-39(64)12-6-23-3-9-26(61)10-4-23/h1-17,34-37,41-52,54-59,66-77H,18-21H2,(H3-,60,61,62,63,64,65)/p+1/t34-,35-,36-,37-,41-,42-,43-,44-,45+,46+,47+,48+,49-,50-,51-,52-,54-,55-,56-,57-/m1/s1
SMILES:	c1cc(ccc1C=CC(=[O+]C[C@@H]1[C@H]([C@@H]([C@H]([C@H](Oc2cc(cc(c2O)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](COC(=O)C=Cc3ccc(cc3)O)O2)O)O)O)c2c(cc3-c(cc(cc3=O)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)o2)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)O1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003681] Flavonoid 3p-O-p-coumaroyl glycosides [CHEMONTID:0002709] Anthocyanidin 3p-O-p-coumaroyl glycosides [CHEMONTID:0002713] Anthocyanidin 3p-O-6-p-coumaroyl glycosides

*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
NPO5532	Staurocucumis liouvillei	Species	Cucumariidae	Eukaryota	n.a.	n.a.	n.a.	PMID[11421733]
NPO4573	Mortierella alpina	Species	Mortierellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12191843]
NPO4057	Picrolemma pseudocoffea	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[6533270]
NPO4573	Mortierella alpina	Species	Mortierellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9668087]
NPO20960	Anchistea virginica	Species	Blechnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO324	Dianella nigra	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20960	Anchistea virginica	Species	Blechnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5755	Bauhinia glauca	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20186	Xanthomonas campestris	Species	Xanthomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO6176	Ramichloridium apiculatum	Species	Dissoconiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4573	Mortierella alpina	Species	Mortierellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5532	Staurocucumis liouvillei	Species	Cucumariidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO145	Chondropetalum andreaeanum	Species	Restionaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4057	Picrolemma pseudocoffea	Species	n.a.	n.a.	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 NPC207281 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	481
0.1-0.2	1911
0.2-0.3	4416
0.3-0.4	9343
0.4-0.5	8313
0.5-0.6	5367
0.6-0.7	5900
0.7-0.8	5243
0.8-0.85	890
0.85-0.9	542
0.9-0.95	270
0.95-1	21

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 NPC207281 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	420
0.1-0.2	1003
0.2-0.3	2203
0.3-0.4	2669
0.4-0.5	1758
0.5-0.6	740
0.6-0.7	231
0.7-0.8	100
0.8-0.85	17
0.85-0.9	3
0.9-0.95	6
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