NPASS Compound

Natural Product: NPC187632

Natural Product ID	NPC187632
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	UDDACPSXBDFIFN-NSGUDPGQSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3581893
PubChem CID	16138413
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000238] Tannins [CHEMONTID:0001710] Hydrolyzable tannins

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

Chemical Representations

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24 1 0 24 25 2 0 25 26 1 0 26 27 2 0 27 28 1 0 28 29 2 0 29 30 1 0 30 31 2 0 31 32 1 0 30 33 1 0 29 34 1 0 27 35 1 0 35 36 2 0 35 37 1 0 24 38 1 0 23 39 1 0 22 40 1 0 15 41 1 0 41 42 1 0 42 43 1 0 43 44 1 0 44 45 1 0 45 46 2 0 45 47 1 0 47 48 2 0 48 49 1 0 49 50 2 0 50 51 1 0 51 52 2 0 52 53 1 0 53 54 1 0 54 55 2 0 55 56 1 0 56 57 2 0 57 58 1 0 58 59 2 0 59 60 1 0 58 61 1 0 56 62 1 0 62 63 2 0 62 64 1 0 64 65 1 0 65 66 1 0 66 67 1 0 67 68 1 0 68 69 1 0 69 70 1 0 70 71 1 0 71 72 1 0 72 73 2 0 72 74 1 0 74 75 2 0 75 76 1 0 76 77 2 0 77 78 1 0 78 79 2 0 79 80 1 0 80 81 2 0 81 82 1 0 82 83 2 0 83 84 1 0 84 85 2 0 85 86 1 0 84 87 1 0 83 88 1 0 81 89 1 0 89 90 2 0 89 91 1 0 78 92 1 0 77 93 1 0 76 94 1 0 69 95 1 0 67 96 1 0 96 97 1 0 97 98 2 0 97 99 1 0 99100 2 0 100101 1 0 101102 2 0 102103 1 0 103104 2 0 103105 1 0 102106 1 0 101107 1 0 66108 1 0 108109 1 0 109110 2 0 109111 1 0 111112 2 0 112113 1 0 113114 2 0 114115 1 0 115116 2 0 116117 1 0 117118 1 0 118119 2 0 119120 1 0 120121 2 0 121122 1 0 122123 2 0 123124 1 0 122125 1 0 121126 1 0 126127 1 0 127128 2 0 128129 1 0 129130 2 0 130131 1 0 131132 2 0 132133 1 0 131134 1 0 129135 1 0 135136 2 0 135137 1 0 137138 1 0 138139 1 0 139140 1 0 140141 1 0 141142 1 0 142143 1 0 143144 1 0 144145 1 0 145146 2 0 145147 1 0 147148 2 0 148149 1 0 149150 2 0 150151 1 0 151152 2 0 152153 1 0 153154 2 0 154155 1 0 155156 2 0 156157 1 0 157158 2 0 158159 1 0 157160 1 0 156161 1 0 154162 1 0 162163 2 0 162164 1 0 151165 1 0 150166 1 0 149167 1 0 142168 1 0 140169 1 0 169170 1 0 170171 2 0 170172 1 0 172173 2 0 173174 1 0 174175 2 0 175176 1 0 176177 2 0 176178 1 0 175179 1 0 174180 1 0 139181 1 0 181182 1 0 182183 2 0 115184 1 0 114185 1 0 113186 1 0 51187 1 0 50188 1 0 49189 1 0 42190 1 0 190191 1 0 191192 2 0 191193 1 0 193194 2 0 194195 1 0 195196 2 0 196197 1 0 197198 2 0 197199 1 0 196200 1 0 195201 1 0 6 1 1 0 43 13 1 0 52 47 1 0 59 54 1 0 95 65 1 0 104 99 1 0 116111 1 0 123118 1 0 132127 1 0 168138 1 0 177172 1 0 198193 1 0 37 14 1 0 91 68 1 0 182120 1 0 25 20 1 0 31 26 1 0 79 74 1 0 85 80 1 0 164141 1 0 152147 1 0 158153 1 0 1202 1 0 3203 1 0 7204 1 0 8205 1 0 9206 1 0 13207 1 6 14208 1 1 15209 1 6 16210 1 0 16211 1 0 21212 1 0 28213 1 0 32214 1 0 33215 1 0 34216 1 0 38217 1 0 39218 1 0 40219 1 0 42220 1 6 43221 1 1 48222 1 0 55223 1 0 57224 1 0 60225 1 0 61226 1 0 65227 1 1 66228 1 6 67229 1 1 68230 1 6 69231 1 1 70232 1 0 70233 1 0 75234 1 0 82235 1 0 86236 1 0 87237 1 0 88238 1 0 92239 1 0 93240 1 0 94241 1 0 100242 1 0 104243 1 0 105244 1 0 106245 1 0 107246 1 0 112247 1 0 119248 1 0 124249 1 0 125250 1 0 128251 1 0 130252 1 0 133253 1 0 134254 1 0 138255 1 1 139256 1 6 140257 1 1 141258 1 6 142259 1 1 143260 1 0 143261 1 0 148262 1 0 155263 1 0 159264 1 0 160265 1 0 161266 1 0 165267 1 0 166268 1 0 167269 1 0 173270 1 0 177271 1 0 178272 1 0 179273 1 0 180274 1 0 184275 1 0 185276 1 0 186277 1 0 187278 1 0 188279 1 0 189280 1 0 194281 1 0 198282 1 0 199283 1 0 200284 1 0 201285 1 0 M END

Standard InCHIKey	UDDACPSXBDFIFN-NSGUDPGQSA-N
Standard InCHI	InChI=1S/C123H84O78/c124-40-1-25(2-41(125)70(40)142)106(166)193-100-97-61(22-181-112(172)31-13-50(134)76(148)85(157)64(31)67-34(115(175)190-97)16-53(137)79(151)88(67)160)187-121(199-109(169)28-7-46(130)73(145)47(131)8-28)103(100)196-118(178)37-19-56(140)82(154)91(163)94(37)184-58-11-29(9-48(132)74(58)146)110(170)200-122-104(101(194-107(167)26-3-42(126)71(143)43(127)4-26)98-62(188-122)23-182-113(173)32-14-51(135)77(149)86(158)65(32)68-35(116(176)191-98)17-54(138)80(152)89(68)161)197-119(179)38-20-57(141)83(155)92(164)95(38)186-60-21-39-96(93(165)84(60)156)185-59-12-30(10-49(133)75(59)147)111(171)201-123-105(198-120(39)180)102(195-108(168)27-5-44(128)72(144)45(129)6-27)99-63(189-123)24-183-114(174)33-15-52(136)78(150)87(159)66(33)69-36(117(177)192-99)18-55(139)81(153)90(69)162/h1-21,61-63,97-105,121-165H,22-24H2/t61-,62-,63-,97-,98-,99-,100+,101+,102+,103-,104-,105-,121+,122+,123+/m1/s1
SMILES	c1c(cc(c(c1O)O)O)C(=O)O[C@H]1[C@H]2[C@@H](COC(=O)c3cc(c(c(c3-c3c(cc(c(c3O)O)O)C(=O)O2)O)O)O)O[C@H]([C@@H]1OC(=O)c1cc(c(c(c1Oc1cc(cc(c1O)O)C(=O)O[C@H]1[C@@H]([C@H]([C@H]2[C@@H](COC(=O)c3cc(c(c(c3-c3c(cc(c(c3O)O)O)C(=O)O2)O)O)O)O1)OC(=O)c1cc(c(c(c1)O)O)O)OC(=O)c1cc(c(c(c1Oc1cc2c(c(c1O)O)Oc1cc(cc(c1O)O)C(=O)O[C@H]1[C@@H]([C@H]([C@H]3[C@@H](COC(=O)c4cc(c(c(c4-c4c(cc(c(c4O)O)O)C(=O)O3)O)O)O)O1)OC(=O)c1cc(c(c(c1)O)O)O)OC2=O)O)O)O)O)O)O)OC(=O)c1cc(c(c(c1)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	2808.26	Volume:	2475.171 ? Van der Waals volume.
Dense:	1.135	LogP:	-2.252 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-4.388 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.932 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	25.0	Rigid Bonds:	155.0
TPSA:	1299.54 ? Topological Polar Surface Area.	H-Bond Acceptor:	78.0
H-Bond Donor:	42.0	Rings:	22.0
Heavy Atoms:	78.0

MedChem Properties

QED Drug-Likeness Score:	0.026	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	9.406	Fsp³:	0.146
MCE-18:	537.128 ? 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:	1	PAINS Alert:	1
Colloidal aggregators:	1.0	Fluc inhibitor:	0.104 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.356 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.667 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.799	Promiscuous compounds:	0.969

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-11.847	MDCK Permeability:	-4.397
Pgp-inhibitor:	0.0	Pgp-substrate:	0.0
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):	0.0
20% Bioavailability (F20%):	0.999	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	1.0
Plasma Protein Binding (PPB):	71.814%	Volume Distribution (VD):	0.051
Fu:	5.296% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.955
OATP1B3 inhibitor:	0.263	BCRP inhibitor:	0.0
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:	0.873
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
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):

2.079

Half-life (T1/2):

15.62

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	1.0
Human Hepatotoxicity (H-HT):	0.062	Drug-induced Liver Injury (DILI):	1.0
AMES Toxicity:	1.0	Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.999	Skin Sensitization:	1.0
Carcinogencity:	0.003	Eye Corrosion:	0.0
Eye Irritation:	0.005	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.0	Drug-induced Nephrotoxicity:	0.001
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.0
A549 Cytotoxicity:	1.0	Hek293 Cytotoxicity:	0.801
BCF:	-2.576 ? 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:	2.957 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	3.576 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.372 ? 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
NPO20417	Tamarix nilotica	Species	Tamaricaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20405847]
NPO20417	Tamarix nilotica	Species	Tamaricaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23675651]
NPO33012	myricaria bracteata	Species	Tamaricaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25918997]
NPO20417	Tamarix nilotica	Species	Tamaricaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[26938659]
NPO20786	Tamarix tetrandra	Species	Tamaricaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[26938659]
NPO20417	Tamarix nilotica	Species	Tamaricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20786	Tamarix tetrandra	Species	Tamaricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO33012	myricaria bracteata	Species	Tamaricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20417	Tamarix nilotica	Species	Tamaricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20417	Tamarix nilotica	Species	Tamaricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20786	Tamarix tetrandra	Species	Tamaricaceae	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

Activity Type	# Activity
CC50	4

Activity Type	# Activity
Cell line	4

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
NPT116	Cell line	HL-60	Homo sapiens	CC50	=	16400.0	nM	PMID[26938659]
NPT2394	Cell line	HSC-4	Homo sapiens	CC50	=	34300.0	nM	PMID[26938659]
NPT2385	Cell line	HSC-3	Homo sapiens	CC50	=	25500.0	nM	PMID[26938659]
NPT924	Cell line	HSC-2	Homo sapiens	CC50	=	18800.0	nM	PMID[26938659]

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 NPC187632 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	29319
0.1-0.2	20158
0.2-0.3	259
0.3-0.4	53
0.4-0.5	24
0.5-0.6	10
0.6-0.7	6
0.7-0.8	0
0.8-0.85	9
0.85-0.9	8
0.9-0.95	2
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC240200
0.9221	High Similarity	NPC223534
0.9	High Similarity	NPC488885
0.8831	High Similarity	NPC40078
0.878	High Similarity	NPC194439
0.878	High Similarity	NPC33724
0.8736	High Similarity	NPC469652
0.8736	High Similarity	NPC486025
0.8736	High Similarity	NPC486024
0.8539	High Similarity	NPC93065
0.8539	High Similarity	NPC220876
0.8395	Intermediate Similarity	NPC290289
0.8372	Intermediate Similarity	NPC488884
0.8276	Intermediate Similarity	NPC488887
0.8276	Intermediate Similarity	NPC488886
0.8272	Intermediate Similarity	NPC483712
0.8272	Intermediate Similarity	NPC158214
0.8272	Intermediate Similarity	NPC97924
0.8272	Intermediate Similarity	NPC214202
0.8022	Intermediate Similarity	NPC260521
0.7805	Intermediate Similarity	NPC112211
0.7805	Intermediate Similarity	NPC254925
0.7579	Intermediate Similarity	NPC31208
0.7579	Intermediate Similarity	NPC160543
0.7363	Intermediate Similarity	NPC471091
0.7172	Intermediate Similarity	NPC174140
0.7021	Intermediate Similarity	NPC469649
0.6974	Remote Similarity	NPC43918
0.6974	Remote Similarity	NPC261411
0.6974	Remote Similarity	NPC190204
0.6883	Remote Similarity	NPC469651
0.6842	Remote Similarity	NPC47521
0.6421	Remote Similarity	NPC116108
0.5699	Remote Similarity	NPC269625
0.5584	Remote Similarity	NPC114791
0.5584	Remote Similarity	NPC104222
0.5584	Remote Similarity	NPC210501
0.5584	Remote Similarity	NPC318826
0.5584	Remote Similarity	NPC141331
0.5465	Remote Similarity	NPC149300
0.5333	Remote Similarity	NPC8940
0.5098	Remote Similarity	NPC189312
0.5046	Remote Similarity	NPC201814

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC187632 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6788
0.1-0.2	2357
0.2-0.3	5
0.3-0.4	0
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