NPASS Compound

Natural Product: NPC483413

Natural Product ID	NPC483413
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	ZVEIDTIRZJGYDY-MMPHDZEQSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	44559737
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003533] Flavonoid-7-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 86 90 0 0 0 0 0 0 0 0999 V2000 -6.4507 3.5898 0.6077 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3123 2.5284 1.6409 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.3890 1.4825 1.6032 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.2864 0.7109 0.3251 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9303 0.4756 -0.2085 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.8188 1.3520 0.3159 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1075 1.8486 1.5962 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7006 0.5893 0.4318 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4773 0.4358 -0.0466 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7151 -0.5935 0.5453 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4291 -0.8891 0.1713 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1355 -0.1266 -0.8414 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5971 0.8785 -1.4247 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9143 1.1766 -1.0390 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6122 2.1772 -1.6439 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3297 2.0364 -2.8573 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0281 1.6223 -2.4210 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4174 -0.4351 -1.1994 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9724 0.2194 -2.1030 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1139 -1.4833 -0.5579 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4958 -2.1971 0.4272 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1004 -3.3169 1.1631 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2005 -3.9631 0.7181 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7344 -4.9955 1.5059 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1737 -5.3541 2.6905 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0599 -4.6828 3.1150 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5089 -3.6784 2.3891 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4541 -5.0248 4.3318 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6918 -6.3820 3.4907 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2448 -1.8532 0.7413 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3996 -1.7161 -0.9855 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4542 -0.8320 -0.5624 C 0 0 1 0 0 0 0 0 0 0 0 0 5.2852 -1.3402 0.5518 C 0 0 1 0 0 0 0 0 0 0 0 0 6.5326 -0.5274 0.7752 C 0 0 1 0 0 0 0 0 0 0 0 0 6.5422 0.6955 -0.0928 C 0 0 2 0 0 0 0 0 0 0 0 0 6.3470 0.1361 -1.5196 C 0 0 2 0 0 0 0 0 0 0 0 0 6.5610 1.2572 -2.4873 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1514 -0.4497 -1.6729 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7730 1.3491 -0.1139 O 0 0 0 0 0 0 0 0 0 0 0 0 8.0070 2.6938 0.0662 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0219 3.4309 0.2740 O 0 0 0 0 0 0 0 0 0 0 0 0 9.3941 3.2694 0.0175 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6209 -0.2009 2.1357 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5372 -1.3422 1.7730 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9975 0.6936 -1.6060 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.1895 1.2203 -0.6595 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.2652 0.4990 -1.0818 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.4660 -0.6465 -0.5895 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.2599 0.9569 -2.1075 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1092 0.5914 2.6618 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9886 3.2567 -0.3042 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9640 4.4769 1.0742 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4637 3.9472 0.3075 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3699 2.9987 2.6460 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4007 1.8974 1.6857 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7052 -0.3163 0.5819 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6254 -0.6139 -0.1428 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6611 2.1983 -0.3840 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1335 -1.2071 1.3430 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6863 2.2278 -3.7425 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2609 2.6349 -2.8944 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6261 0.9703 -2.9315 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0784 1.2745 -3.3530 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6772 -3.7372 -0.2176 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6097 -5.4935 1.1305 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6383 -3.1186 2.6757 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7554 -5.7602 4.3572 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6040 -6.7343 3.2710 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9250 0.0763 -0.1630 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5512 -2.3977 0.3272 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4139 -1.1719 0.5590 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6888 1.3537 0.0949 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2205 -0.5837 -1.6184 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7575 0.7740 -3.4902 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6516 1.8836 -2.5218 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4513 1.8696 -2.1893 H 0 0 0 0 0 0 0 0 0 0 0 0 10.0954 2.4147 -0.0910 H 0 0 0 0 0 0 0 0 0 0 0 0 9.6165 3.9221 0.8612 H 0 0 0 0 0 0 0 0 0 0 0 0 9.4541 3.8271 -0.9556 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8948 0.4748 2.3113 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0596 -1.7496 2.4952 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7037 0.1341 -2.0167 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.2862 0.7021 -1.7872 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.1014 2.0516 -2.2071 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.9633 0.4918 -3.0666 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7482 1.1396 3.3969 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 1 0 6 8 1 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 1 0 13 17 1 0 12 18 1 0 18 19 2 0 18 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 24 25 2 0 25 26 1 0 26 27 2 0 26 28 1 0 25 29 1 0 21 30 1 0 20 31 1 0 31 32 1 0 32 33 1 0 33 34 1 0 34 35 1 0 35 36 1 0 36 37 1 0 36 38 1 0 35 39 1 0 39 40 1 0 40 41 2 0 40 42 1 0 34 43 1 0 33 44 1 0 5 45 1 0 4 46 1 0 46 47 1 0 47 48 2 0 47 49 1 0 3 50 1 0 7 2 1 0 14 9 1 0 27 22 1 0 38 32 1 0 30 11 1 0 1 51 1 0 1 52 1 0 1 53 1 0 2 54 1 1 3 55 1 1 4 56 1 1 5 57 1 6 6 58 1 6 10 59 1 0 16 60 1 0 16 61 1 0 16 62 1 0 17 63 1 0 23 64 1 0 24 65 1 0 27 66 1 0 28 67 1 0 29 68 1 0 32 69 1 1 33 70 1 6 34 71 1 6 35 72 1 1 36 73 1 6 37 74 1 0 37 75 1 0 37 76 1 0 42 77 1 0 42 78 1 0 42 79 1 0 43 80 1 0 44 81 1 0 45 82 1 0 49 83 1 0 49 84 1 0 49 85 1 0 50 86 1 0 M END

Standard InCHIKey	ZVEIDTIRZJGYDY-MMPHDZEQSA-N
Standard InCHI	InChI=1S/C32H36O18/c1-10-20(37)29(47-13(4)34)25(42)32(44-10)49-18-9-17-19(21(38)28(18)43-5)22(39)30(27(48-17)14-6-7-15(35)16(36)8-14)50-31-24(41)23(40)26(11(2)45-31)46-12(3)33/h6-11,20,23-26,29,31-32,35-38,40-42H,1-5H3/t10-,11-,20-,23-,24+,25+,26-,29+,31-,32-/m0/s1
SMILES	C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)Oc1cc2c(c(c1OC)O)c(=O)c(c(c1ccc(c(c1)O)O)o2)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)OC(=O)C)O)O)O)OC(=O)C)O

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO9114	Kalanchoe brasiliensis	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16724848]
NPO9114	Kalanchoe brasiliensis	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7853000]
NPO9114	Kalanchoe brasiliensis	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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

Activity Type	# Activity
IC50	1

Activity Type	# Activity
Non-molecular	1

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
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	=	0.25	ug.mL-1	PMID[7853000]

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 NPC483413 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	15409
0.1-0.2	31569
0.2-0.3	2209
0.3-0.4	405
0.4-0.5	209
0.5-0.6	42
0.6-0.7	4
0.7-0.8	0
0.8-0.85	0
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8621	High Similarity	NPC483416
0.8506	High Similarity	NPC483415
0.7826	Intermediate Similarity	NPC483412
0.6818	Remote Similarity	NPC27640
0.6771	Remote Similarity	NPC483414
0.6484	Remote Similarity	NPC488071
0.62	Remote Similarity	NPC606657
0.5962	Remote Similarity	NPC470446
0.5957	Remote Similarity	NPC159579
0.5957	Remote Similarity	NPC129217
0.5914	Remote Similarity	NPC52550
0.5789	Remote Similarity	NPC182121
0.5745	Remote Similarity	NPC305811
0.5745	Remote Similarity	NPC271692
0.567	Remote Similarity	NPC209023
0.5648	Remote Similarity	NPC470451
0.5455	Remote Similarity	NPC488072
0.5417	Remote Similarity	NPC24043
0.5408	Remote Similarity	NPC21666
0.54	Remote Similarity	NPC265115
0.5361	Remote Similarity	NPC59534
0.5357	Remote Similarity	NPC18772
0.5327	Remote Similarity	NPC473073
0.5327	Remote Similarity	NPC471669
0.5278	Remote Similarity	NPC470449
0.5278	Remote Similarity	NPC470445
0.5243	Remote Similarity	NPC471748
0.5214	Remote Similarity	NPC488078
0.5208	Remote Similarity	NPC127546
0.5208	Remote Similarity	NPC57625
0.5208	Remote Similarity	NPC173637
0.5208	Remote Similarity	NPC317489
0.5208	Remote Similarity	NPC223424
0.5208	Remote Similarity	NPC600591
0.5204	Remote Similarity	NPC42773
0.5204	Remote Similarity	NPC45522
0.52	Remote Similarity	NPC605784
0.5192	Remote Similarity	NPC293626
0.5189	Remote Similarity	NPC75574
0.5152	Remote Similarity	NPC175107
0.5102	Remote Similarity	NPC46420
0.51	Remote Similarity	NPC85707
0.5094	Remote Similarity	NPC126784
0.5094	Remote Similarity	NPC241423
0.5051	Remote Similarity	NPC117260
0.5051	Remote Similarity	NPC201292
0.5048	Remote Similarity	NPC233994
0.5047	Remote Similarity	NPC470443
0.5045	Remote Similarity	NPC470455

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC483413 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5029
0.1-0.2	4074
0.2-0.3	40
0.3-0.4	4
0.4-0.5	3
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