NPASS Compound

Natural Product: NPC7502

Natural Product ID	NPC7502
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	PKGQELPPZCMQGJ-LQPHVJJUSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	6325883
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0004081] Iridoid O-glycosides

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 69 72 0 0 0 0 0 0 0 0999 V2000 -0.4339 -3.4298 -0.3064 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4786 -2.2746 -0.0112 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7671 -2.7193 0.6539 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1848 -1.4486 1.3629 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8860 -1.0717 2.0441 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6239 -2.0780 3.1106 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6020 -2.4616 3.3517 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6052 -1.9156 2.6040 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5063 -1.4334 1.3019 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0952 -1.2342 0.8954 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2401 -0.2869 1.0657 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2595 -0.4431 0.1459 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.6195 -0.2024 0.7443 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2436 1.0862 0.2948 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.2341 1.2962 -1.1876 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2080 0.3890 -1.7878 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.8274 0.9198 -3.1493 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9226 0.0760 -3.8003 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0581 0.2885 -1.0221 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.4742 0.9427 -1.7682 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7002 2.1858 0.9890 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4536 -1.3019 0.5676 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4428 -0.4766 0.4118 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6911 0.0942 0.5319 C 0 0 1 0 0 0 0 0 0 0 0 0 4.4094 -0.0753 -0.7808 C 0 0 1 0 0 0 0 0 0 0 0 0 3.9480 0.9939 -1.7260 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2263 2.3948 -1.1939 C 0 0 2 0 0 0 0 0 0 0 0 0 4.4310 2.2670 0.2804 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3655 3.6143 0.9889 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6714 3.4970 2.3319 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5131 1.4334 0.8875 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2608 3.3085 -1.5397 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5668 0.8760 -1.8594 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7878 -0.1396 -0.6478 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8606 -1.7420 -1.2639 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8572 -3.9328 0.5606 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1952 -3.0742 -1.0433 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1703 -4.1751 -0.8750 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4878 -3.5211 1.3746 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5205 -3.0486 -0.0881 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0179 -1.6109 2.0661 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9639 -0.0499 2.4093 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4358 -2.4692 3.6587 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8237 -3.1827 4.1113 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9595 -2.2249 0.6332 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0196 -0.2530 0.3338 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2367 -1.5060 -0.1770 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4624 -0.1039 1.8586 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3270 1.0418 0.6138 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0910 2.3689 -1.4351 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6514 -0.6262 -1.8489 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7421 1.0988 -3.7449 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3691 1.9280 -2.9938 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3988 -0.3986 -3.1222 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8151 1.6314 -2.3658 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4628 2.8998 0.3183 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1118 -1.3648 1.3261 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2736 -0.3503 1.3929 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0609 -1.0462 -1.2138 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3773 0.8685 -2.7512 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1887 2.7722 -1.6221 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4753 1.9072 0.4340 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0711 4.3416 0.5293 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3496 4.0732 0.9191 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2474 2.6958 2.4390 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5821 3.5049 -0.8746 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0905 1.7055 -1.6885 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1586 0.0177 -1.5633 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4207 -0.8458 -1.3888 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 1 0 9 10 1 0 9 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 16 19 1 0 15 20 1 0 14 21 1 0 13 22 1 0 4 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 28 31 1 0 27 32 1 0 26 33 1 0 25 34 1 0 2 35 1 0 10 2 1 0 19 12 1 0 31 24 1 0 10 5 1 0 1 36 1 0 1 37 1 0 1 38 1 0 3 39 1 0 3 40 1 0 4 41 1 1 5 42 1 1 6 43 1 0 7 44 1 0 9 45 1 6 10 46 1 6 12 47 1 6 13 48 1 1 14 49 1 1 15 50 1 1 16 51 1 6 17 52 1 0 17 53 1 0 18 54 1 0 20 55 1 0 21 56 1 0 22 57 1 0 24 58 1 1 25 59 1 6 26 60 1 6 27 61 1 6 28 62 1 6 29 63 1 0 29 64 1 0 30 65 1 0 32 66 1 0 33 67 1 0 34 68 1 0 35 69 1 0 M END

Standard InCHIKey	PKGQELPPZCMQGJ-LQPHVJJUSA-N
Standard InCHI	InChI=1S/C21H34O14/c1-21(30)4-8(32-19-16(28)14(26)12(24)9(5-22)33-19)7-2-3-31-18(11(7)21)35-20-17(29)15(27)13(25)10(6-23)34-20/h2-3,7-20,22-30H,4-6H2,1H3/t7-,8+,9+,10+,11+,12-,13+,14-,15-,16+,17+,18-,19+,20-,21?/m0/s1
SMILES	CC1(C[C@H]([C@@H]2C=CO[C@H]([C@H]12)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O[C@H]1[C@@H]([C@H]([C@H]([C@@H](CO)O1)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	510.19	Volume:	457.973 ? Van der Waals volume.
Dense:	1.114	LogP:	-2.269 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-1.37 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-0.606 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	22.0
TPSA:	228.22 ? Topological Polar Surface Area.	H-Bond Acceptor:	14.0
H-Bond Donor:	9.0	Rings:	4.0
Heavy Atoms:	14.0

MedChem Properties

QED Drug-Likeness Score:	0.163	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.271	Fsp³:	0.905
MCE-18:	81.2 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.392	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.036 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.001 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.461	Promiscuous compounds:	0.209

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.665	MDCK Permeability:	-5.074
Pgp-inhibitor:	0.0	Pgp-substrate:	0.925
PAMPA:	1.0 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.998
20% Bioavailability (F20%):	0.689	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.005	MRP1:	0.103
Plasma Protein Binding (PPB):	32.037%	Volume Distribution (VD):	-0.534
Fu:	69.094% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.996
OATP1B3 inhibitor:	0.998	BCRP inhibitor:	0.001
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.058
HLM stability:	0.0 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

0.89

Half-life (T1/2):

2.803

ADMET: Toxicity

hERG Blockers:	0.003	hERG Blockers (10um):	0.017
Human Hepatotoxicity (H-HT):	0.678	Drug-induced Liver Injury (DILI):	0.898
AMES Toxicity:	0.994	Rat Oral Acute Toxicity:	0.009
Maximum Recommended Daily Dose:	0.001	Skin Sensitization:	1.0
Carcinogencity:	0.249	Eye Corrosion:	0.0
Eye Irritation:	0.045	Respiratory Toxicity:	0.003
Drug-induced Neurotoxicity:	0.007	Ototoxicity:	0.994
Hematotoxicity:	0.772	Drug-induced Nephrotoxicity:	0.871
Genotoxicity:	0.207	RPMI-8226 Immunitoxicity:	0.152
A549 Cytotoxicity:	0.818	Hek293 Cytotoxicity:	0.255
BCF:	0.337 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	2.449 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	3.891 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.156 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	Roots	n.a.	n.a.	PMID[22916954]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	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	Organism Name	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

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC7502 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	22729
0.1-0.2	23656
0.2-0.3	2955
0.3-0.4	436
0.4-0.5	57
0.5-0.6	16
0.6-0.7	5
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC485190
0.7541	Intermediate Similarity	NPC485186
0.7541	Intermediate Similarity	NPC485187
0.6607	Remote Similarity	NPC259296
0.6607	Remote Similarity	NPC98276
0.6429	Remote Similarity	NPC145287
0.6081	Remote Similarity	NPC233500
0.6	Remote Similarity	NPC219656
0.5921	Remote Similarity	NPC282551
0.5921	Remote Similarity	NPC196130
0.5902	Remote Similarity	NPC107594
0.5844	Remote Similarity	NPC470685
0.5696	Remote Similarity	NPC219804
0.5696	Remote Similarity	NPC163783
0.5593	Remote Similarity	NPC171484
0.5593	Remote Similarity	NPC149018
0.5422	Remote Similarity	NPC161125
0.5312	Remote Similarity	NPC50464
0.5246	Remote Similarity	NPC220167
0.5135	Remote Similarity	NPC470683
0.5135	Remote Similarity	NPC470684
0.5135	Remote Similarity	NPC270737
0.5079	Remote Similarity	NPC258501
0.5079	Remote Similarity	NPC151308

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC7502 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7260
0.1-0.2	1806
0.2-0.3	64
0.3-0.4	20
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
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
		NPD

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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