NPASS Compound

Structure

NPC132857 OpenBabel06302216072D 63 68 0 0 1 0 0 0 0 0999 V2000 -2.3695 -0.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4799 0.2344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3730 1.1999 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.3078 1.4642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7224 0.5857 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1061 2.0178 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.6727 1.2287 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5982 1.5238 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6036 2.4952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6814 2.8005 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.9714 3.7277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9336 3.5942 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9446 4.6987 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.8980 4.8849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6040 5.6085 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.2865 6.5799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1278 6.0942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1278 5.1228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9691 4.6370 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8104 5.1228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8104 6.0942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9691 6.5799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6517 4.6370 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -9.4930 5.1228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6517 3.6656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9864 6.3583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6244 7.0909 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1588 6.8670 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.8168 7.5817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5268 8.5089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5789 8.7213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2889 9.6485 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9209 8.0066 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2109 7.0795 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2454 6.9726 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6331 6.5580 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.3294 5.8807 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.1122 6.4560 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0053 7.4215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7880 7.9968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6777 7.6066 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7845 6.6411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0018 6.0657 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7681 5.0139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6952 5.3039 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9015 4.0517 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7153 3.0983 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.6250 2.7576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2295 2.2570 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4970 1.6190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4030 1.2534 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.0057 0.7914 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9794 1.6394 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.6596 -0.2769 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7499 -0.6176 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5900 -1.5757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3198 -1.9164 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0696 -1.2988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9098 -0.3406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.3398 -2.1933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4095 -0.8945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0189 7.9074 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 3 2 1 6 0 0 0 3 4 1 0 0 0 0 3 51 1 0 0 0 0 4 5 2 0 0 0 0 4 6 1 0 0 0 0 6 10 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 10 9 1 1 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 13 15 1 0 0 0 0 15 16 1 6 0 0 0 15 26 1 0 0 0 0 16 17 1 0 0 0 0 17 22 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 23 1 0 0 0 0 21 22 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 28 34 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 34 33 1 6 0 0 0 34 35 1 0 0 0 0 35 36 2 3 0 0 0 35 63 1 0 0 0 0 36 37 1 0 0 0 0 37 38 1 6 0 0 0 37 44 1 0 0 0 0 38 43 2 0 0 0 0 38 39 1 0 0 0 0 39 40 2 0 0 0 0 40 41 1 0 0 0 0 41 42 2 0 0 0 0 42 43 1 0 0 0 0 44 45 2 0 0 0 0 44 46 1 0 0 0 0 46 47 1 0 0 0 0 47 48 1 1 0 0 0 47 49 1 0 0 0 0 49 50 1 0 0 0 0 49 53 1 6 0 0 0 50 51 2 3 0 0 0 50 52 1 0 0 0 0 53 54 2 3 0 0 0 54 55 1 0 0 0 0 54 62 1 0 0 0 0 55 60 2 0 0 0 0 55 56 1 0 0 0 0 56 57 2 0 0 0 0 56 61 1 0 0 0 0 57 58 1 0 0 0 0 58 59 2 0 0 0 0 59 60 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	972.49
Volume:	938.207
LogP:	0.729
LogD:	0.978
LogS:	-3.532
# Rotatable Bonds:	11
TPSA:	332.28
# H-Bond Aceptor:	20
# H-Bond Donor:	12
# Rings:	8
# Heavy Atoms:	20

MedChem Properties

QED Drug-Likeness Score:	0.072
Synthetic Accessibility Score:	6.387
Fsp3:	0.917
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.39
MDCK Permeability:	8.673926640767604e-05
Pgp-inhibitor:	0.761
Pgp-substrate:	0.221
Human Intestinal Absorption (HIA):	0.994
20% Bioavailability (F20%):	0.049
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.172
Plasma Protein Binding (PPB):	57.27577209472656%
Volume Distribution (VD):	0.301
Pgp-substrate:	18.5557804107666%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.497
CYP2C19-inhibitor:	0.001
CYP2C19-substrate:	0.113
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.01
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.042
CYP3A4-inhibitor:	0.066
CYP3A4-substrate:	0.004

ADMET: Excretion

Clearance (CL):	0.552
Half-life (T1/2):	0.731

ADMET: Toxicity

hERG Blockers:	0.053
Human Hepatotoxicity (H-HT):	0.189
Drug-inuced Liver Injury (DILI):	0.012
AMES Toxicity:	0.102
Rat Oral Acute Toxicity:	0.133
Maximum Recommended Daily Dose:	0.021
Skin Sensitization:	0.054
Carcinogencity:	0.223
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.933

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC132857

Natural Product ID:	NPC132857
*Common Name:**	YGXCETJZBDTKRY-ITDJUSPCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YGXCETJZBDTKRY-ITDJUSPCSA-N
Standard InCHI:	InChI=1S/C45H54N8O10/c1-6-31-42(59)52-22-11-14-32(52)43(60)51(5)34(24-27-16-18-29(19-17-27)50(3)4)44(61)53-23-20-30(54)25-33(53)39(56)49-37(28-12-8-7-9-13-28)45(62)63-26(2)36(40(57)47-31)48-41(58)38-35(55)15-10-21-46-38/h7-10,12-13,15-19,21,26,31-34,36-37,55H,6,11,14,20,22-25H2,1-5H3,(H,47,57)(H,48,58)(H,49,56)/t26-,31+,32-,33+,34+,36-,37+/m0/s1
SMILES:	CC[C@@H]1C(=O)N2CCC[C@H]2C(=O)N(C)[C@H](Cc2ccc(cc2)N(C)C)C(=O)N2CCC(=O)C[C@@H]2C(=N[C@H](c2ccccc2)C(=O)O[C@@H](C)[C@@H](C(=N1)O)N=C(c1c(cccn1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0001813] Peptidomimetics [CHEMONTID:0001961] Depsipeptides [CHEMONTID:0001994] Cyclic depsipeptides

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO9360	Hydrangea macrophylla	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7663	Carex pendula	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9360	Hydrangea macrophylla	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9360	Hydrangea macrophylla	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9360	Hydrangea macrophylla	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3349	Cryptosporiopsis abietina	Species	Dermateaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9360	Hydrangea macrophylla	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7663	Carex pendula	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10141	Alstonia lenormandii	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7227	Nepeta tuberosa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2225	Neonauclea sessilifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO184	Halobates hayanus	Species	Gerridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3157	Polysyncraton echinatum	Species	Didemnidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9874	Gueriniella serratulae	Species	Monophlebidae	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	NP ID	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

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

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC132857 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	326
0.1-0.2	1680
0.2-0.3	9759
0.3-0.4	11124
0.4-0.5	14203
0.5-0.6	3214
0.6-0.7	2231
0.7-0.8	154
0.8-0.85	1
0.85-0.9	1
0.9-0.95	3
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID

Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC132857 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	186
0.1-0.2	529
0.2-0.3	724
0.3-0.4	1427
0.4-0.5	2587
0.5-0.6	2521
0.6-0.7	1103
0.7-0.8	71
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage

Bioactivity similarity: Similar Natural Products in NPASS

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