NPASS Compound

Structure

NPC208640 OpenBabel06302215342D 40 46 0 0 1 0 0 0 0 0999 V2000 0.0015 -1.7532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5053 -0.8771 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.5176 -0.8779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0245 -0.0018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5191 0.8753 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.4896 0.9764 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -3.1663 0.2236 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6933 1.9307 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.8487 2.4193 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.8490 3.3955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5397 3.3950 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -4.3858 3.8831 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -4.3860 4.8599 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2321 5.3480 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0779 4.8594 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.9234 5.3476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7686 4.8589 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -7.7683 3.8822 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.9228 3.3940 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0776 3.8827 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0773 2.8750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2316 3.3945 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -5.2313 2.4184 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3852 1.9302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5394 2.4188 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5391 1.4112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6137 3.3939 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.3393 4.0471 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.2678 3.7453 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.9934 4.3984 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -10.7905 5.3534 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.8621 5.6552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.1365 5.0020 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.5162 6.0065 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.9218 4.0966 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.4706 2.7903 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6348 5.3586 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1230 1.7670 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5069 0.8762 0.0000 O 0 0 0 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 1 2 1 0 0 0 0 2 40 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 38 1 0 0 0 0 5 6 1 0 0 0 0 5 39 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 8 25 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 9 38 1 0 0 0 0 10 11 1 0 0 0 0 11 25 1 0 0 0 0 11 12 1 0 0 0 0 12 22 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 15 14 1 1 0 0 0 15 16 1 0 0 0 0 15 20 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 37 1 0 0 0 0 18 19 1 0 0 0 0 18 27 1 6 0 0 0 19 20 1 0 0 0 0 20 21 1 6 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 6 0 0 0 28 27 1 1 0 0 0 28 29 1 0 0 0 0 28 33 1 0 0 0 0 29 30 1 0 0 0 0 29 36 1 6 0 0 0 30 31 1 0 0 0 0 30 35 1 1 0 0 0 31 32 1 0 0 0 0 31 34 1 6 0 0 0 32 33 1 0 0 0 0 39 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	564.37
Volume:	572.455
LogP:	3.399
LogD:	3.328
LogS:	-4.33
# Rotatable Bonds:	2
TPSA:	117.84
# H-Bond Aceptor:	8
# H-Bond Donor:	4
# Rings:	7
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.378
Synthetic Accessibility Score:	5.861
Fsp3:	1.0
Lipinski Rule-of-5:	Accepted
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:	-4.97
MDCK Permeability:	3.734412166522816e-05
Pgp-inhibitor:	0.964
Pgp-substrate:	0.131
Human Intestinal Absorption (HIA):	0.02
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.229

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.012
Plasma Protein Binding (PPB):	96.1867904663086%
Volume Distribution (VD):	0.746
Pgp-substrate:	2.9553096294403076%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.728
CYP2C19-inhibitor:	0.006
CYP2C19-substrate:	0.794
CYP2C9-inhibitor:	0.046
CYP2C9-substrate:	0.038
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.356
CYP3A4-inhibitor:	0.057
CYP3A4-substrate:	0.196

ADMET: Excretion

Clearance (CL):	8.416
Half-life (T1/2):	0.114

ADMET: Toxicity

hERG Blockers:	0.753
Human Hepatotoxicity (H-HT):	0.187
Drug-inuced Liver Injury (DILI):	0.06
AMES Toxicity:	0.147
Rat Oral Acute Toxicity:	0.545
Maximum Recommended Daily Dose:	0.844
Skin Sensitization:	0.949
Carcinogencity:	0.048
Eye Corrosion:	0.003
Eye Irritation:	0.008
Respiratory Toxicity:	0.965

Download Data

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

Natural Product: NPC208640

Natural Product ID:	NPC208640
*Common Name:**	KKQQPVXVNRLUKV-PDBRICLWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KKQQPVXVNRLUKV-PDBRICLWSA-N
Standard InCHI:	InChI=1S/C32H52O8/c1-16-7-10-32(38-14-16)17(2)26-24(40-32)12-21-19-6-5-18-11-22(33)25(39-29-28(36)27(35)23(34)15-37-29)13-31(18,4)20(19)8-9-30(21,26)3/h16-29,33-36H,5-15H2,1-4H3/t16?,17?,18-,19?,20?,21?,22?,23-,24?,25+,26?,27+,28-,29+,30+,31+,32?/m1/s1
SMILES:	CC1CCC2(C(C)C3C(CC4C5CC[C@@H]6CC([C@H](C[C@]6(C)C5CC[C@]34C)O[C@H]3[C@@H]([C@H]([C@@H](CO3)O)O)O)O)O2)OC1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11968320
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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO22077	Dioscorea tokoro	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22077	Dioscorea tokoro	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22077	Dioscorea tokoro	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22077	Dioscorea tokoro	Species	Dioscoreaceae	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 NPC208640 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	567
0.1-0.2	5171
0.2-0.3	14206
0.3-0.4	10269
0.4-0.5	5667
0.5-0.6	3502
0.6-0.7	1974
0.7-0.8	877
0.8-0.85	201
0.85-0.9	117
0.9-0.95	47
0.95-1	99

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 NPC208640 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	546
0.1-0.2	4670
0.2-0.3	2797
0.3-0.4	593
0.4-0.5	336
0.5-0.6	158
0.6-0.7	32
0.7-0.8	15
0.8-0.85	0
0.85-0.9	2
0.9-0.95	0
0.95-1	1

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