NPASS Compound

Structure

NPC66924 OpenBabel06302215552D 64 69 0 0 1 0 0 0 0 0999 V2000 -3.0541 -2.6981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0541 -2.6981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5541 -1.8321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5595 -1.7275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1096 -2.4707 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3516 -0.7494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1032 -1.0842 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4064 -1.5606 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5170 -2.1145 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.4201 -2.6709 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1287 -3.1547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3300 -3.6590 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0061 -4.0855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3646 -5.0143 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5435 -4.0077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0957 -4.0657 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5024 -4.9793 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4220 -3.6166 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9306 -3.3711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3162 -2.9585 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8420 -2.7804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5933 -3.4403 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5405 -3.1196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9507 -2.2360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8979 -1.9153 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5336 -1.8697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3361 -1.3405 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9608 -0.9185 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2177 -0.2494 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.5267 -2.4344 0.0000 N 0 5 0 0 0 0 0 0 0 0 0 0 -0.8590 -3.6618 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.3177 -3.5005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3197 -3.8024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9387 -3.0170 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6904 -4.7311 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6801 -4.8745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0641 -2.3992 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9239 -2.9099 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7960 -2.4206 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8083 -1.4206 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6804 -0.9314 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9485 -0.9100 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9608 0.0899 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1010 0.6005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1133 1.6005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9855 2.0898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7465 2.1111 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7341 3.1110 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5939 3.6217 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5816 4.6216 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7095 5.1109 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4414 5.1322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4291 6.1321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2889 6.6428 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2766 7.6427 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4045 8.1320 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1364 8.1533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1241 9.1532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9839 9.6639 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9715 10.6638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0994 11.1531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8313 11.1744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0709 -1.8441 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9430 -1.3548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 28 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 4 6 1 0 0 0 0 6 29 1 0 0 0 0 6 7 2 3 0 0 0 7 8 1 0 0 0 0 8 63 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 3 0 0 0 10 37 1 0 0 0 0 11 32 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 33 1 1 0 0 0 13 14 2 0 0 0 0 13 15 1 0 0 0 0 15 32 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 2 3 0 0 0 18 31 1 0 0 0 0 19 20 1 0 0 0 0 20 30 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 21 24 1 0 0 0 0 22 23 1 0 0 0 0 24 25 1 0 0 0 0 24 26 2 0 0 0 0 26 27 1 0 0 0 0 26 30 1 0 0 0 0 27 28 2 3 0 0 0 28 29 1 0 0 0 0 31 32 2 0 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 35 36 1 0 0 0 0 37 38 1 1 0 0 0 37 63 1 0 0 0 0 38 39 1 0 0 0 0 39 40 1 0 0 0 0 40 41 2 0 0 0 0 40 42 1 0 0 0 0 42 43 1 0 0 0 0 43 44 1 0 0 0 0 44 45 2 0 0 0 0 45 46 1 0 0 0 0 45 47 1 0 0 0 0 47 48 1 0 0 0 0 48 49 1 0 0 0 0 49 50 1 0 0 0 0 50 51 1 6 0 0 0 50 52 1 0 0 0 0 52 53 1 0 0 0 0 53 54 1 0 0 0 0 54 55 1 0 0 0 0 55 56 1 6 0 0 0 55 57 1 0 0 0 0 57 58 1 0 0 0 0 58 59 1 0 0 0 0 59 60 1 0 0 0 0 60 61 1 0 0 0 0 60 62 1 0 0 0 0 63 64 1 6 0 0 0 M CHG 1 30 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	870.57
Volume:	956.888
LogP:	11.566
LogD:	8.516
LogS:	-6.316
# Rotatable Bonds:	21
TPSA:	132.83
# H-Bond Aceptor:	9
# H-Bond Donor:	4
# Rings:	6
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.042
Synthetic Accessibility Score:	7.48
Fsp3:	0.509
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.973
MDCK Permeability:	7.00048394719488e-06
Pgp-inhibitor:	0.995
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.081
20% Bioavailability (F20%):	0.976
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.005
Plasma Protein Binding (PPB):	101.89171600341797%
Volume Distribution (VD):	0.941
Pgp-substrate:	0.7845423221588135%

ADMET: Metabolism

CYP1A2-inhibitor:	0.566
CYP1A2-substrate:	0.835
CYP2C19-inhibitor:	0.65
CYP2C19-substrate:	0.53
CYP2C9-inhibitor:	0.949
CYP2C9-substrate:	0.431
CYP2D6-inhibitor:	0.936
CYP2D6-substrate:	0.072
CYP3A4-inhibitor:	0.874
CYP3A4-substrate:	0.91

ADMET: Excretion

Clearance (CL):	2.772
Half-life (T1/2):	0.034

ADMET: Toxicity

hERG Blockers:	0.901
Human Hepatotoxicity (H-HT):	0.431
Drug-inuced Liver Injury (DILI):	0.844
AMES Toxicity:	0.622
Rat Oral Acute Toxicity:	0.94
Maximum Recommended Daily Dose:	0.992
Skin Sensitization:	0.964
Carcinogencity:	0.114
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.987

Download Data

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

Natural Product: NPC66924

Natural Product ID:	NPC66924
*Common Name:**	QBDWVXAZHXTFSD-DFJNACPPSA-M
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QBDWVXAZHXTFSD-DFJNACPPSA-M
Standard InCHI:	InChI=1S/C55H73N4O5/c1-13-39-35(8)42-28-44-37(10)41(24-25-48(60)64-27-26-34(7)23-17-22-33(6)21-16-20-32(5)19-15-18-31(3)4)52(58-44)50-51(55(62)63-12)54(61)49-38(11)45(59-53(49)50)30-47-40(14-2)36(9)43(57-47)29-46(39)56-42/h13,26,28-33,37,41,51H,1,14-25,27H2,2-12H3,(H-,56,57,58,59,61)/q-1/p-1/b34-26+/t32-,33-,37+,41+,51-/m1/s1
SMILES:	C=Cc1c(C)c2=CC3=NC(=C4[C@H](C(=O)C5=C(C)C(=Cc6c(CC)c(C)c(C=c1[nH]2)[n-]6)N=C45)C(=O)OC)[C@@H](CCC(=O)OC/C=C(C)/CCC[C@H](C)CCC[C@H](C)CCCC(C)C)[C@@H]3C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001455] Tetrapyrroles and derivatives [CHEMONTID:0000716] Chlorins

*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
NPO17780	Curcuma heyneana	Species	Zingiberaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[23387824]
NPO13153	Callicarpa macrophylla	Species	Lamiaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[26110519]
NPO13153	Callicarpa macrophylla	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11837	Codonopsis clematidea	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20907	Costus afer	Species	Costaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13153	Callicarpa macrophylla	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15465	Mikania microptera	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17780	Curcuma heyneana	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10359	Chaiturus marrubiastrum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15038	Withania adpressa	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15789	Leucas cephalotes	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1547	Symphytum uplandicum	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13153	Callicarpa macrophylla	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11837	Codonopsis clematidea	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3719	Potamophylax latipennis	Species	Limnephilidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20907	Costus afer	Species	Costaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17627	Senecio rufus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16940	Phebalium ralstonii	Species	Rutaceae	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 NPC66924 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	343
0.1-0.2	2079
0.2-0.3	8876
0.3-0.4	20404
0.4-0.5	6837
0.5-0.6	2805
0.6-0.7	1261
0.7-0.8	83
0.8-0.85	1
0.85-0.9	6
0.9-0.95	2
0.95-1	0

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 NPC66924 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	225
0.1-0.2	632
0.2-0.3	784
0.3-0.4	2220
0.4-0.5	3234
0.5-0.6	1756
0.6-0.7	271
0.7-0.8	13
0.8-0.85	10
0.85-0.9	4
0.9-0.95	1
0.95-1	0

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