NPASS Compound

Structure

NPC304971 OpenBabel06302215192D 75 82 0 0 1 0 0 0 0 0999 V2000 -2.9420 -5.5104 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9420 -5.5104 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4420 -4.6444 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4475 -4.5399 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2396 -3.5617 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1056 -3.0617 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3135 -2.0836 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5704 -1.4144 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7783 -0.4363 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7294 -0.1273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9373 0.8509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8883 1.1599 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.6315 0.4908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4236 -0.4874 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4725 -0.7964 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.2157 -1.4655 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2646 -1.7746 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0077 -2.4437 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7998 -3.4218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8488 -3.7308 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7998 -4.0399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0962 2.1380 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3531 2.8072 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4020 2.4982 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.6589 3.1673 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8668 4.1454 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8179 4.4544 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.0258 5.4326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2826 6.1017 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5610 3.7853 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1237 4.8146 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3316 5.7927 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4116 6.4618 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2037 7.4400 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.7474 7.7490 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4905 7.0799 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.4416 7.3889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2826 6.1017 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9553 8.7272 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9468 8.1091 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3626 6.1528 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2922 2.8583 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1941 1.5200 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2431 1.2110 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0352 0.2328 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9159 -0.0762 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.6590 0.5930 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.4511 1.5711 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.1943 2.2402 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5001 1.8801 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6101 0.2839 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1238 -1.0543 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7783 -0.4363 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 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 4.3301 -1.5000 0.0000 C 0 0 2 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 3.4641 -0.0000 0.0000 C 0 0 1 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 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 3 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 -2.5981 -0.5000 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 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2562 -2.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 3 2 1 6 0 0 0 3 4 1 0 0 0 0 3 20 1 0 0 0 0 4 5 1 0 0 0 0 4 54 1 6 0 0 0 6 5 1 6 0 0 0 6 7 1 0 0 0 0 6 20 1 0 0 0 0 7 8 1 1 0 0 0 7 17 1 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 15 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 22 1 6 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 6 0 0 0 15 17 1 0 0 0 0 17 18 1 6 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 6 0 0 0 23 22 1 6 0 0 0 23 24 1 0 0 0 0 23 30 1 0 0 0 0 24 25 1 0 0 0 0 24 43 1 0 0 0 0 25 26 1 0 0 0 0 25 42 1 6 0 0 0 26 27 1 0 0 0 0 26 31 1 1 0 0 0 27 28 1 0 0 0 0 27 30 1 0 0 0 0 28 29 1 0 0 0 0 32 31 1 6 0 0 0 32 33 1 0 0 0 0 32 38 1 0 0 0 0 33 34 1 0 0 0 0 33 41 1 1 0 0 0 34 35 1 0 0 0 0 34 40 1 0 0 0 0 35 36 1 0 0 0 0 35 39 1 6 0 0 0 36 37 1 0 0 0 0 36 38 1 0 0 0 0 44 43 1 6 0 0 0 44 45 1 0 0 0 0 44 50 1 0 0 0 0 45 46 1 0 0 0 0 45 53 1 6 0 0 0 46 47 1 0 0 0 0 46 52 1 0 0 0 0 47 48 1 0 0 0 0 47 51 1 6 0 0 0 48 49 1 0 0 0 0 48 50 1 0 0 0 0 54 55 1 0 0 0 0 55 56 2 0 0 0 0 55 57 1 0 0 0 0 57 58 1 1 0 0 0 57 74 1 0 0 0 0 58 59 1 0 0 0 0 59 60 1 6 0 0 0 59 61 1 0 0 0 0 61 62 1 0 0 0 0 63 62 1 1 0 0 0 63 64 1 0 0 0 0 63 70 1 0 0 0 0 64 65 1 0 0 0 0 64 73 1 0 0 0 0 65 66 1 0 0 0 0 65 72 1 1 0 0 0 66 67 1 0 0 0 0 66 71 1 6 0 0 0 67 68 1 0 0 0 0 67 70 1 0 0 0 0 68 69 1 0 0 0 0 74 75 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	1076.58
Volume:	1044.904
LogP:	1.96
LogD:	2.52
LogS:	-3.415
# Rotatable Bonds:	18
TPSA:	335.06
# H-Bond Aceptor:	22
# H-Bond Donor:	12
# Rings:	8
# Heavy Atoms:	22

MedChem Properties

QED Drug-Likeness Score:	0.059
Synthetic Accessibility Score:	6.935
Fsp3:	0.925
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:	-6.187
MDCK Permeability:	0.0005009955493733287
Pgp-inhibitor:	0.09
Pgp-substrate:	0.98
Human Intestinal Absorption (HIA):	0.998
20% Bioavailability (F20%):	0.006
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.085
Plasma Protein Binding (PPB):	50.29411315917969%
Volume Distribution (VD):	-0.038
Pgp-substrate:	15.066557884216309%

ADMET: Metabolism

CYP1A2-inhibitor:	0.0
CYP1A2-substrate:	0.085
CYP2C19-inhibitor:	0.001
CYP2C19-substrate:	0.067
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.006
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.053
CYP3A4-inhibitor:	0.015
CYP3A4-substrate:	0.022

ADMET: Excretion

Clearance (CL):	0.224
Half-life (T1/2):	0.649

ADMET: Toxicity

hERG Blockers:	0.554
Human Hepatotoxicity (H-HT):	0.173
Drug-inuced Liver Injury (DILI):	0.037
AMES Toxicity:	0.096
Rat Oral Acute Toxicity:	0.656
Maximum Recommended Daily Dose:	0.055
Skin Sensitization:	0.316
Carcinogencity:	0.255
Eye Corrosion:	0.003
Eye Irritation:	0.004
Respiratory Toxicity:	0.967

Download Data

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

Natural Product: NPC304971

Natural Product ID:	NPC304971
*Common Name:**	IPXVHJDKAPENOM-RBZYLCDESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IPXVHJDKAPENOM-RBZYLCDESA-N
Standard InCHI:	InChI=1S/C53H88O22/c1-9-29-33(68-23(3)32(66-8)16-22(2)21-67-48-42(62)41(61)38(58)34(19-54)72-48)18-31-28-11-10-26-17-27(12-14-52(26,6)30(28)13-15-53(29,31)7)71-51-47(75-50-44(64)40(60)37(57)25(5)70-50)45(65)46(35(20-55)73-51)74-49-43(63)39(59)36(56)24(4)69-49/h10,22,24-25,27-51,54-65H,3,9,11-21H2,1-2,4-8H3/t22-,24?,25?,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+,53-/m1/s1
SMILES:	CC[C@H]1[C@H](C[C@H]2[C@@H]3CC=C4C[C@H](CC[C@]4(C)[C@H]3CC[C@]12C)O[C@H]1C([C@H]([C@@H](C(CO)O1)O[C@H]1[C@@H](C([C@H](C(C)O1)O)O)O)O)O[C@H]1[C@H](C([C@H](C(C)O1)O)O)O)OC(=C)[C@H](C[C@@H](C)CO[C@H]1C([C@H]([C@@H](C(CO)O1)O)O)O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	52931427
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001013] Steroidal glycosides [CHEMONTID:0002364] Steroidal 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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO24833	Dioscorea polystachya	Species	Dioscoreaceae	Eukaryota	n.a.	bark	n.a.	PMID[24689699]
NPO14409	Dioscorea nipponica	Species	Dioscoreaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[23707257]
NPO1103	Dioscorea japonica	Species	Dioscoreaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[21353549]
NPO14376	Stephania cephalantha	Species	Menispermaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21214233]
NPO14376	Stephania cephalantha	Species	Menispermaceae	Eukaryota	n.a.	stem	n.a.	PMID[21214233]
NPO7395	Tribulus terrestris	Species	Zygophyllaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[11141122]
NPO15018.1	Dioscorea collettii var. hypoglauca	Varieties	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10075765]
NPO9089	Dioscorea panthaica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24833	Dioscorea polystachya	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1103	Dioscorea japonica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Showing 1 to 10 of 51 entries

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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☑ 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 NPC304971 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	295
0.1-0.2	2005
0.2-0.3	5943
0.3-0.4	13246
0.4-0.5	9543
0.5-0.6	6117
0.6-0.7	3178
0.7-0.8	1577
0.8-0.85	407
0.85-0.9	262
0.9-0.95	121
0.95-1	3

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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 NPC304971 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	236
0.1-0.2	2113
0.2-0.3	4189
0.3-0.4	1767
0.4-0.5	464
0.5-0.6	278
0.6-0.7	76
0.7-0.8	15
0.8-0.85	4
0.85-0.9	8
0.9-0.95	0
0.95-1	0

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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