NPASS Compound

Natural Product: NPC171932

Natural Product ID	NPC171932
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Catechin-(3'->0->3''')-Afzelechin
IUPAC Name	(2R,3S)-2-[4-hydroxy-3-[2-hydroxy-5-[(2R,3S)-3,5,7-trihydroxy-3,4-dihydro-2H-chromen-2-yl]phenoxy]phenyl]-3,4-dihydro-2H-chromene-3,5,7-triol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL499952
PubChem CID	11272988
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0000337] Flavans [CHEMONTID:0003012] Flavan-3-ols [CHEMONTID:0001584] Catechins

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 67 72 0 0 0 0 0 0 0 0999 V2000 -2.7746 0.1736 2.3602 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4444 0.3739 2.6527 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4822 -0.0823 1.7836 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8623 -0.7370 0.6268 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2185 -0.9249 0.3578 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2078 -0.4795 1.2083 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6540 -0.6771 0.9339 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.9349 -1.0474 -0.4959 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.2820 -0.7084 -1.0010 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1480 0.0971 -0.1323 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5035 0.2477 -0.4336 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.2849 1.0116 0.3947 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7858 1.6373 1.5134 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4486 1.4928 1.8172 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6523 0.7191 0.9803 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2932 0.5560 1.2674 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.5978 2.4084 2.3404 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.9946 -0.3899 -1.5674 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7278 -2.4386 -0.6608 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1314 -1.1870 -0.2313 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0409 -0.3275 -0.8238 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4012 -0.4634 -0.6005 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2763 0.4028 -1.2019 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7757 1.3943 -2.0196 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4199 1.5502 -2.2581 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5624 0.6762 -1.6491 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8100 0.7830 -1.8507 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7425 0.3336 -1.0207 C 0 0 2 0 0 0 0 0 0 0 0 0 5.3600 -0.8426 -1.7662 C 0 0 2 0 0 0 0 0 0 0 0 0 6.8541 -0.7139 -1.6985 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3213 -0.3812 -0.3315 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6918 -0.5095 -0.0573 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1674 -0.2094 1.2003 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3015 0.2156 2.1863 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9591 0.3334 1.8905 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4458 0.0409 0.6394 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1010 0.1574 0.3380 O 0 0 0 0 0 0 0 0 0 0 0 0 8.7518 0.5229 3.4542 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5734 -0.9360 -1.0409 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8893 -0.8789 -3.0690 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8826 0.0949 2.0328 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5464 0.5257 3.0320 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1758 0.8800 3.5490 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4660 -1.4431 -0.5567 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0784 -1.4438 1.6096 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1763 -0.5608 -1.1863 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1980 -0.1949 -2.0049 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8400 -1.6642 -1.2350 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.3491 1.1421 0.1762 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0005 1.9687 2.6935 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.2775 1.8992 2.9232 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.6494 -1.1662 -1.4142 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5559 -2.8844 -0.3176 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7843 -1.2363 0.0369 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4577 2.0987 -2.5110 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0340 2.3317 -2.9021 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2251 1.4144 -2.4961 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2396 1.2494 -1.3879 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9944 -1.7608 -1.2638 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2671 -1.7451 -1.9080 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2573 -0.0300 -2.4668 H 0 0 0 0 0 0 0 0 0 0 0 0 10.2463 -0.3201 1.3853 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2312 0.6668 2.6386 H 0 0 0 0 0 0 0 0 0 0 0 0 9.7285 0.7339 3.6523 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2414 -0.9372 -2.0017 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2668 -1.6370 -3.2367 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2471 0.8254 2.5992 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 13 17 1 0 11 18 1 0 8 19 1 0 4 20 1 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 24 25 1 0 25 26 2 0 26 27 1 0 23 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 2 0 32 33 1 0 33 34 2 0 34 35 1 0 35 36 2 0 36 37 1 0 34 38 1 0 32 39 1 0 29 40 1 0 3 41 1 0 6 1 1 0 16 7 1 0 26 21 1 0 37 28 1 0 15 10 1 0 36 31 1 0 1 42 1 0 2 43 1 0 5 44 1 0 7 45 1 1 8 46 1 6 9 47 1 0 9 48 1 0 12 49 1 0 14 50 1 0 17 51 1 0 18 52 1 0 19 53 1 0 22 54 1 0 24 55 1 0 25 56 1 0 27 57 1 0 28 58 1 6 29 59 1 1 30 60 1 0 30 61 1 0 33 62 1 0 35 63 1 0 38 64 1 0 39 65 1 0 40 66 1 0 41 67 1 0 M END

Standard InCHIKey	QDQUMKMBQVBHBC-BAAZAXTHSA-N
Standard InCHI	InChI=1S/C30H26O11/c31-15-7-21(35)17-11-23(37)29(40-25(17)9-15)13-1-3-19(33)27(5-13)39-28-6-14(2-4-20(28)34)30-24(38)12-18-22(36)8-16(32)10-26(18)41-30/h1-10,23-24,29-38H,11-12H2/t23-,24-,29+,30+/m0/s1
SMILES	c1cc(c(cc1[C@@H]1[C@H](Cc2c(cc(cc2O1)O)O)O)Oc1cc(ccc1O)[C@@H]1[C@H](Cc2c(cc(cc2O1)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	562.15	Volume:	541.152 ? Van der Waals volume.
Dense:	1.039	LogP:	1.285 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.617 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.984 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	34.0
TPSA:	189.53 ? Topological Polar Surface Area.	H-Bond Acceptor:	11.0
H-Bond Donor:	8.0	Rings:	6.0
Heavy Atoms:	11.0

MedChem Properties

QED Drug-Likeness Score:	0.181	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.249	Fsp³:	0.2
MCE-18:	120.0 ? 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:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.753	Fluc inhibitor:	0.323 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.602 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.472 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.48	Promiscuous compounds:	0.22

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.863	MDCK Permeability:	-4.979
Pgp-inhibitor:	0.001	Pgp-substrate:	0.209
PAMPA:	0.16 ? 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):	0.0
20% Bioavailability (F20%):	0.511	30% Bioavailability (F30%):	0.997
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.005	MRP1:	0.941
Plasma Protein Binding (PPB):	94.219%	Volume Distribution (VD):	0.172
Fu:	6.702% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	0.999	BCRP inhibitor:	0.105
BSEP inhibitor:	0.145

ADMET: Metabolism

CYP1A2-inhibitor:	0.088	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.01	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.014	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.013	CYP3A4-substrate:	0.03
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
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):

9.012

Half-life (T1/2):

3.321

ADMET: Toxicity

hERG Blockers:	0.189	hERG Blockers (10um):	0.657
Human Hepatotoxicity (H-HT):	0.809	Drug-induced Liver Injury (DILI):	0.492
AMES Toxicity:	0.516	Rat Oral Acute Toxicity:	0.487
Maximum Recommended Daily Dose:	0.969	Skin Sensitization:	0.814
Carcinogencity:	0.195	Eye Corrosion:	0.0
Eye Irritation:	0.808	Respiratory Toxicity:	0.838
Drug-induced Neurotoxicity:	0.099	Ototoxicity:	0.71
Hematotoxicity:	0.047	Drug-induced Nephrotoxicity:	0.344
Genotoxicity:	0.994	RPMI-8226 Immunitoxicity:	0.174
A549 Cytotoxicity:	0.949	Hek293 Cytotoxicity:	0.983
BCF:	1.036 ? 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:	3.339 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.454 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.96 ? 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
NPO32566	periploca aphylla	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10869229]
NPO32566	periploca aphylla	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15387640]

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
Others	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
NPT2	Others	Unspecified	n.a.	IC50	=	19700.0	nM	PubChem BioAssay data set

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 NPC171932 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	24600
0.1-0.2	20759
0.2-0.3	4062
0.3-0.4	291
0.4-0.5	101
0.5-0.6	21
0.6-0.7	9
0.7-0.8	2
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.7797	Intermediate Similarity	NPC28440
0.7736	Intermediate Similarity	NPC16435
0.74	Intermediate Similarity	NPC207179
0.74	Intermediate Similarity	NPC167571
0.74	Intermediate Similarity	NPC278552
0.7115	Intermediate Similarity	NPC261619
0.7115	Intermediate Similarity	NPC61477
0.7115	Intermediate Similarity	NPC78770
0.7115	Intermediate Similarity	NPC219876
0.7115	Intermediate Similarity	NPC126029
0.7115	Intermediate Similarity	NPC15658
0.6727	Remote Similarity	NPC61946
0.6481	Remote Similarity	NPC47398
0.6481	Remote Similarity	NPC234333
0.6481	Remote Similarity	NPC260898
0.6415	Remote Similarity	NPC268266
0.6415	Remote Similarity	NPC42760
0.6415	Remote Similarity	NPC220825
0.6415	Remote Similarity	NPC268342
0.6406	Remote Similarity	NPC308402
0.5455	Remote Similarity	NPC58190
0.5455	Remote Similarity	NPC108811
0.5455	Remote Similarity	NPC9636
0.5455	Remote Similarity	NPC170103
0.5455	Remote Similarity	NPC236202
0.5455	Remote Similarity	NPC262911
0.5455	Remote Similarity	NPC202742
0.5373	Remote Similarity	NPC246202
0.5373	Remote Similarity	NPC224161
0.5373	Remote Similarity	NPC46335
0.5373	Remote Similarity	NPC279406
0.5373	Remote Similarity	NPC486519
0.5224	Remote Similarity	NPC277331
0.5224	Remote Similarity	NPC100482
0.5211	Remote Similarity	NPC211561
0.5147	Remote Similarity	NPC294558
0.5147	Remote Similarity	NPC18185
0.5147	Remote Similarity	NPC263940
0.5088	Remote Similarity	NPC482472
0.5077	Remote Similarity	NPC477841
0.5068	Remote Similarity	NPC278548

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC171932 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4760
0.1-0.2	4296
0.2-0.3	83
0.3-0.4	6
0.4-0.5	3
0.5-0.6	0
0.6-0.7	0
0.7-0.8	2
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
0.7115	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.7115	Intermediate Similarity	NPD1613	Phase 4

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