NPASS Compound

Natural Product: NPC12244

Natural Product ID	NPC12244
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	AMUAOTIJXYEFIP-VIUVDTKASA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	57390787
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0000507] Isoflavonoid 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 66 69 0 0 0 0 0 0 0 0999 V2000 4.4465 0.3956 -4.0944 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8669 0.1934 -2.8241 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6900 0.0276 -1.7039 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0711 0.0567 -1.8060 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8971 -0.1065 -0.7017 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3406 -0.3051 0.5445 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9620 -0.3381 0.6713 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1670 -0.1726 -0.4449 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7276 -0.2133 -0.2716 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0807 -1.4219 -0.3767 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7685 -1.4518 -0.2175 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0780 -0.3695 0.0352 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3068 -0.4867 0.1901 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0787 0.6142 0.4559 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4761 1.8684 0.5736 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1122 2.0007 0.4236 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6536 0.8724 0.1545 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0198 0.9525 -0.0038 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5657 2.0608 0.0985 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4807 3.2366 0.5398 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2877 2.9464 0.8408 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5794 3.3476 2.1661 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4173 0.5475 0.6128 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2946 -0.5344 0.5559 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.9916 -0.6031 1.9053 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.4937 -0.4194 1.7245 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.9183 -1.4961 0.7180 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.1894 -1.2449 -0.5593 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.2097 -0.7472 -1.5792 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.2442 -1.6906 -1.7297 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2082 -0.2700 -0.4657 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5012 -2.7107 1.2615 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7511 0.7989 1.1304 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8068 -1.9105 2.3976 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1766 -0.4668 1.6387 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5986 -0.6714 2.9222 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2814 -0.0778 -0.8008 O 0 0 0 0 0 0 0 0 0 0 0 0 8.9910 0.1135 -1.9910 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8956 1.4018 -4.1905 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7158 0.2873 -4.9137 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2879 -0.3283 -4.2909 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5302 0.2106 -2.7686 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5133 -0.4944 1.6516 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6343 -2.3253 -0.5848 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7694 -1.4653 0.0973 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8889 3.6193 1.3622 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4324 2.5232 2.8968 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9139 4.1790 2.5103 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6130 3.7534 2.2187 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7280 -1.4563 0.3426 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5916 0.1208 2.6308 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9905 -0.5568 2.6920 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0272 -1.4736 0.5840 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8003 -2.2093 -0.9408 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7004 0.1827 -1.2404 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7277 -0.5252 -2.5545 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2680 -1.9482 -2.6862 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9734 -3.4791 0.8371 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1429 1.5124 1.4335 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8568 -2.1563 2.1790 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7943 0.0723 3.1339 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3452 -0.5713 3.7269 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2182 -1.7095 2.9406 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9537 0.6286 -1.7080 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4911 0.7678 -2.7125 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2703 -0.8846 -2.4216 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 2 0 16 20 1 0 15 21 1 0 21 22 1 0 14 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 6 35 1 0 35 36 1 0 5 37 1 0 37 38 1 0 8 3 1 0 18 9 1 0 31 24 1 0 17 12 1 0 1 39 1 0 1 40 1 0 1 41 1 0 4 42 1 0 7 43 1 0 10 44 1 0 13 45 1 0 20 46 1 0 22 47 1 0 22 48 1 0 22 49 1 0 24 50 1 6 25 51 1 1 26 52 1 1 27 53 1 6 28 54 1 6 29 55 1 0 29 56 1 0 30 57 1 0 32 58 1 0 33 59 1 0 34 60 1 0 36 61 1 0 36 62 1 0 36 63 1 0 38 64 1 0 38 65 1 0 38 66 1 0 M END

Standard InCHIKey	AMUAOTIJXYEFIP-VIUVDTKASA-N
Standard InCHI	InChI=1S/C25H28O13/c1-32-12-6-14(34-3)13(33-2)5-10(12)11-9-36-15-7-16(24(35-4)21(29)18(15)19(11)27)37-25-23(31)22(30)20(28)17(8-26)38-25/h5-7,9,17,20,22-23,25-26,28-31H,8H2,1-4H3/t17-,20-,22+,23-,25-/m1/s1
SMILES	COc1cc(c(cc1c1coc2cc(c(c(c2c1=O)O)OC)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)OC)OC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	536.15	Volume:	499.912 ? Van der Waals volume.
Dense:	1.072	LogP:	0.693 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.141 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.696 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	8.0	Rigid Bonds:	24.0
TPSA:	186.74 ? Topological Polar Surface Area.	H-Bond Acceptor:	13.0
H-Bond Donor:	5.0	Rings:	4.0
Heavy Atoms:	13.0

MedChem Properties

QED Drug-Likeness Score:	0.266	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.054	Fsp³:	0.4
MCE-18:	92.0 ? 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:	0
Chelating Alert:	1	PAINS Alert:	0
Colloidal aggregators:	0.476	Fluc inhibitor:	0.211 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.468 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.706 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.081	Promiscuous compounds:	0.503

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.042	MDCK Permeability:	-5.322
Pgp-inhibitor:	0.041	Pgp-substrate:	0.187
PAMPA:	0.107 ? 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):	0.813
20% Bioavailability (F20%):	0.027	30% Bioavailability (F30%):	0.685
50% Bioavailability (F50%):	0.976

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001	MRP1:	0.424
Plasma Protein Binding (PPB):	82.347%	Volume Distribution (VD):	-0.253
Fu:	17.725% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.959
BSEP inhibitor:	0.058

ADMET: Metabolism

CYP1A2-inhibitor:	0.578	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.182	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.023	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.002
CYP3A4-inhibitor:	0.016	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.05
HLM stability:	0.079 ? 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):

2.798

Half-life (T1/2):

3.951

ADMET: Toxicity

hERG Blockers:	0.031	hERG Blockers (10um):	0.132
Human Hepatotoxicity (H-HT):	0.745	Drug-induced Liver Injury (DILI):	0.972
AMES Toxicity:	0.844	Rat Oral Acute Toxicity:	0.055
Maximum Recommended Daily Dose:	0.105	Skin Sensitization:	0.958
Carcinogencity:	0.475	Eye Corrosion:	0.0
Eye Irritation:	0.087	Respiratory Toxicity:	0.041
Drug-induced Neurotoxicity:	0.032	Ototoxicity:	0.913
Hematotoxicity:	0.465	Drug-induced Nephrotoxicity:	0.661
Genotoxicity:	0.691	RPMI-8226 Immunitoxicity:	0.21
A549 Cytotoxicity:	0.322	Hek293 Cytotoxicity:	0.318
BCF:	0.389 ? 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:	3.002 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.379 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.605 ? 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
NPO1830	Dalbergia sissoo	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18154272]
NPO1830	Dalbergia sissoo	Species	Fabaceae	Eukaryota	leaves	n.a.	n.a.	PMID[22212722]
NPO1830	Dalbergia sissoo	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1830	Dalbergia sissoo	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1830	Dalbergia sissoo	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1830	Dalbergia sissoo	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1830	Dalbergia sissoo	Species	Fabaceae	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 NPC12244 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	20231
0.1-0.2	25822
0.2-0.3	2752
0.3-0.4	820
0.4-0.5	186
0.5-0.6	38
0.6-0.7	3
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8	Intermediate Similarity	NPC224462
0.7867	Intermediate Similarity	NPC205076
0.7692	Intermediate Similarity	NPC48773
0.7564	Intermediate Similarity	NPC307518
0.7294	Intermediate Similarity	NPC257714
0.6463	Remote Similarity	NPC481043
0.642	Remote Similarity	NPC73511
0.6098	Remote Similarity	NPC105511
0.593	Remote Similarity	NPC607201
0.5904	Remote Similarity	NPC197896
0.5904	Remote Similarity	NPC313163
0.5882	Remote Similarity	NPC609451
0.5854	Remote Similarity	NPC135345
0.5833	Remote Similarity	NPC186807
0.5833	Remote Similarity	NPC603655
0.5765	Remote Similarity	NPC100720
0.5714	Remote Similarity	NPC156457
0.5714	Remote Similarity	NPC234739
0.5682	Remote Similarity	NPC479407
0.5663	Remote Similarity	NPC45165
0.5647	Remote Similarity	NPC105025
0.5632	Remote Similarity	NPC229729
0.5632	Remote Similarity	NPC21666
0.5595	Remote Similarity	NPC58053
0.5581	Remote Similarity	NPC117260
0.5581	Remote Similarity	NPC201292
0.5568	Remote Similarity	NPC602805
0.5529	Remote Similarity	NPC161749
0.5517	Remote Similarity	NPC479402
0.5517	Remote Similarity	NPC80140
0.5517	Remote Similarity	NPC488071
0.5506	Remote Similarity	NPC488072
0.5393	Remote Similarity	NPC479406
0.5349	Remote Similarity	NPC258035
0.5287	Remote Similarity	NPC24043
0.5281	Remote Similarity	NPC601607
0.5281	Remote Similarity	NPC605067
0.5227	Remote Similarity	NPC138540
0.5213	Remote Similarity	NPC479405
0.5172	Remote Similarity	NPC93337
0.5169	Remote Similarity	NPC479401
0.5158	Remote Similarity	NPC479404
0.5116	Remote Similarity	NPC160515
0.5114	Remote Similarity	NPC45638
0.5057	Remote Similarity	NPC259070
0.5055	Remote Similarity	NPC607707

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC12244 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5370
0.1-0.2	3697
0.2-0.3	70
0.3-0.4	10
0.4-0.5	2
0.5-0.6	1
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
0.5529	Remote Similarity	NPD4381	Clinical (unspecified phase)

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