NPASS Compound

Structure

NPC86064 OpenBabel07101719252D 46 46 0 0 1 0 0 0 0 0999 V2000 1.8344 7.5490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0886 -2.2061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6056 -3.8592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5563 -0.4713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1311 1.2078 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1098 2.5566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3277 1.0112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4648 2.4406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2802 -4.7284 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7529 -2.3677 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7266 7.0975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7817 6.0990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9445 5.5521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9996 4.5536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1625 4.0066 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9155 -3.4804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3804 2.4612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9312 2.1274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8699 -3.1819 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8590 0.2455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2175 3.0082 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4355 1.4627 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0790 1.6515 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4448 -3.7421 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1629 -1.9660 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1798 -2.8032 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.8106 1.6515 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8896 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4017 0.9158 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.9585 2.1274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4990 -3.4174 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3906 -3.4174 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9722 -0.9966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0826 -0.9966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9448 2.2920 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.4448 -3.7421 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.7099 -2.8032 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.7267 -1.9660 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.4879 0.9158 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.4249 2.4406 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6338 3.0733 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0230 -4.2968 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8666 -4.2968 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9688 -1.0792 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0792 -1.0792 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 11 1 0 0 0 0 2 19 1 0 0 0 0 3 19 1 0 0 0 0 4 20 1 0 0 0 0 5 20 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 21 1 0 0 0 0 16 19 1 0 0 0 0 17 21 1 0 0 0 0 17 22 1 0 0 0 0 18 27 1 0 0 0 0 18 35 1 0 0 0 0 21 6 1 6 0 0 0 22 7 1 6 0 0 0 23 8 1 6 0 0 0 23 29 1 0 0 0 0 23 30 1 0 0 0 0 24 9 1 6 0 0 0 24 31 1 0 0 0 0 24 36 1 0 0 0 0 25 10 1 6 0 0 0 25 34 1 0 0 0 0 25 37 1 0 0 0 0 26 16 1 6 0 0 0 26 32 1 0 0 0 0 26 38 1 0 0 0 0 27 39 2 3 0 0 0 27 40 1 0 0 0 0 28 20 1 6 0 0 0 28 33 1 0 0 0 0 28 39 1 0 0 0 0 29 22 1 1 0 0 0 29 46 1 0 0 0 0 30 35 2 3 0 0 0 30 41 1 0 0 0 0 31 37 2 3 0 0 0 31 42 1 0 0 0 0 32 36 2 3 0 0 0 32 43 1 0 0 0 0 33 38 2 3 0 0 0 33 44 1 0 0 0 0 34 45 2 0 0 0 0 34 46 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	651.46
Volume:	688.76
LogP:	5.607
LogD:	5.182
LogS:	-4.675
# Rotatable Bonds:	11
TPSA:	171.8
# H-Bond Aceptor:	12
# H-Bond Donor:	5
# Rings:	1
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.169
Synthetic Accessibility Score:	5.365
Fsp3:	0.824
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:	-5.406
MDCK Permeability:	2.585447145975195e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.702
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.958
30% Bioavailability (F30%):	0.908

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.067
Plasma Protein Binding (PPB):	79.74419403076172%
Volume Distribution (VD):	0.595
Pgp-substrate:	3.8716652393341064%

ADMET: Metabolism

CYP1A2-inhibitor:	0.006
CYP1A2-substrate:	0.026
CYP2C19-inhibitor:	0.203
CYP2C19-substrate:	0.062
CYP2C9-inhibitor:	0.229
CYP2C9-substrate:	0.011
CYP2D6-inhibitor:	0.009
CYP2D6-substrate:	0.047
CYP3A4-inhibitor:	0.794
CYP3A4-substrate:	0.141

ADMET: Excretion

Clearance (CL):	5.111
Half-life (T1/2):	0.338

ADMET: Toxicity

hERG Blockers:	0.015
Human Hepatotoxicity (H-HT):	0.977
Drug-inuced Liver Injury (DILI):	0.805
AMES Toxicity:	0.006
Rat Oral Acute Toxicity:	0.008
Maximum Recommended Daily Dose:	0.138
Skin Sensitization:	0.248
Carcinogencity:	0.041
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.866

Download Data

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

Natural Product: NPC86064

Natural Product ID:	NPC86064
*Common Name:**	Emericellamide B
IUPAC Name:	(3S,6S,9S,12S,18R,19R)-3,6,18-trimethyl-19-[(2S,4S)-4-methyldecan-2-yl]-9-(2-methylpropyl)-12-propan-2-yl-1-oxa-4,7,10,13,16-pentazacyclononadecane-2,5,8,11,14,17-hexone
Synonyms:
Standard InCHIKey:	MBENBNLUEFQFSL-BFKPYXRSSA-N
Standard InCHI:	InChI=1S/C34H61N5O7/c1-11-12-13-14-15-21(6)17-22(7)29-23(8)30(41)35-18-27(40)39-28(20(4)5)33(44)38-26(16-19(2)3)32(43)36-24(9)31(42)37-25(10)34(45)46-29/h19-26,28-29H,11-18H2,1-10H3,(H,35,41)(H,36,43)(H,37,42)(H,38,44)(H,39,40)/t21-,22-,23+,24-,25-,26-,28-,29+/m0/s1
SMILES:	CCCCCC[C@H](C)C[C@H](C)[C@@H]1[C@@H](C)C(=NCC(=N[C@@H](C(C)C)C(=N[C@@H](CC(C)C)C(=N[C@@H](C)C(=N[C@@H](C)C(=O)O1)O)O)O)O)O
Synthetic Gene Cluster:	BGC0001290;
ChEMBL Identifier:	CHEMBL225054
PubChem CID:	16216152
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
NPO15076	Salinispora arenicola	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	PMID[15916417]
NPO15076	Salinispora arenicola	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	PMID[17253854]
NPO15076	Salinispora arenicola	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	PMID[17323993]
NPO33058	emericella sp.	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17323993]
NPO33058	emericella sp.	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19013822]
NPO15076	Salinispora arenicola	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19117399]
NPO15076	Salinispora arenicola	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	PMID[31313922]
NPO15076	Salinispora arenicola	Species	Micromonosporaceae	Bacteria	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

Activity Type	# Activity
IC50	1
MIC	1

Activity Type	# Activity
Cell Line	1
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT393	Cell Line	HCT-116	Homo sapiens	IC50	=	40000.0	nM	PMID[534583]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	6000.0	nM	PMID[534583]

☑ 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 NPC86064 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	85
0.1-0.2	2923
0.2-0.3	21122
0.3-0.4	14179
0.4-0.5	3642
0.5-0.6	555
0.6-0.7	97
0.7-0.8	60
0.8-0.85	16
0.85-0.9	7
0.9-0.95	7
0.95-1	4

Similarity Score	Similarity Level	Natural Product ID
0.9853	High Similarity	NPC43219
0.913	High Similarity	NPC478256
0.8481	Intermediate Similarity	NPC227051
0.8354	Intermediate Similarity	NPC145748
0.8354	Intermediate Similarity	NPC155670
0.8354	Intermediate Similarity	NPC95478
0.8194	Intermediate Similarity	NPC475808
0.8194	Intermediate Similarity	NPC473985
0.8194	Intermediate Similarity	NPC474299
0.8194	Intermediate Similarity	NPC474298
0.8194	Intermediate Similarity	NPC28348
0.8193	Intermediate Similarity	NPC477729
0.8049	Intermediate Similarity	NPC477728
0.8	Intermediate Similarity	NPC138435
0.7949	Intermediate Similarity	NPC315131
0.7949	Intermediate Similarity	NPC315535
0.7949	Intermediate Similarity	NPC478017
0.7867	Intermediate Similarity	NPC141325
0.7867	Intermediate Similarity	NPC474403
0.7821	Intermediate Similarity	NPC316242
0.7792	Intermediate Similarity	NPC476130
0.7792	Intermediate Similarity	NPC476324
0.7778	Intermediate Similarity	NPC477730
0.76	Intermediate Similarity	NPC476285
0.76	Intermediate Similarity	NPC476291
0.7568	Intermediate Similarity	NPC470110
0.7473	Intermediate Similarity	NPC220234
0.7467	Intermediate Similarity	NPC472579
0.7467	Intermediate Similarity	NPC193280
0.7467	Intermediate Similarity	NPC314273
0.7432	Intermediate Similarity	NPC470109
0.7349	Intermediate Similarity	NPC47135
0.7333	Intermediate Similarity	NPC195165
0.7308	Intermediate Similarity	NPC476248
0.7297	Intermediate Similarity	NPC470108
0.7284	Intermediate Similarity	NPC473984
0.7273	Intermediate Similarity	NPC477200
0.7053	Intermediate Similarity	NPC124554
0.7053	Intermediate Similarity	NPC5864
0.7053	Intermediate Similarity	NPC301148
0.7042	Intermediate Similarity	NPC472578
0.7037	Intermediate Similarity	NPC472594
0.7	Intermediate Similarity	NPC208537
0.7	Intermediate Similarity	NPC270005
0.7	Intermediate Similarity	NPC472595
0.6986	Remote Similarity	NPC477644
0.6962	Remote Similarity	NPC477641
0.6962	Remote Similarity	NPC320865
0.6962	Remote Similarity	NPC477643
0.6941	Remote Similarity	NPC474312
0.6923	Remote Similarity	NPC477642
0.6907	Remote Similarity	NPC124549
0.6905	Remote Similarity	NPC314466
0.6848	Remote Similarity	NPC470283
0.6842	Remote Similarity	NPC474402
0.6804	Remote Similarity	NPC198344
0.6795	Remote Similarity	NPC474812
0.6782	Remote Similarity	NPC476523
0.6765	Remote Similarity	NPC319110
0.6765	Remote Similarity	NPC329181
0.6714	Remote Similarity	NPC270041
0.67	Remote Similarity	NPC171734
0.67	Remote Similarity	NPC67009
0.6667	Remote Similarity	NPC320936
0.6667	Remote Similarity	NPC145627
0.6667	Remote Similarity	NPC193386
0.663	Remote Similarity	NPC315237
0.6622	Remote Similarity	NPC327170
0.6622	Remote Similarity	NPC329564
0.6618	Remote Similarity	NPC80350
0.6579	Remote Similarity	NPC145658
0.6548	Remote Similarity	NPC37681
0.6486	Remote Similarity	NPC316826
0.6486	Remote Similarity	NPC317143
0.6486	Remote Similarity	NPC473599
0.6486	Remote Similarity	NPC321468
0.6486	Remote Similarity	NPC327748
0.6484	Remote Similarity	NPC470284
0.6477	Remote Similarity	NPC323180
0.6476	Remote Similarity	NPC471645
0.6471	Remote Similarity	NPC474833
0.6452	Remote Similarity	NPC62263
0.6452	Remote Similarity	NPC471098
0.6452	Remote Similarity	NPC173763
0.6438	Remote Similarity	NPC317147
0.6438	Remote Similarity	NPC318260
0.6437	Remote Similarity	NPC246005
0.6429	Remote Similarity	NPC322946
0.6413	Remote Similarity	NPC475801
0.6413	Remote Similarity	NPC474593
0.6404	Remote Similarity	NPC175419
0.64	Remote Similarity	NPC471129
0.6383	Remote Similarity	NPC226513
0.6344	Remote Similarity	NPC474576
0.6304	Remote Similarity	NPC322966
0.6264	Remote Similarity	NPC270957
0.6264	Remote Similarity	NPC323958
0.6264	Remote Similarity	NPC321340
0.6264	Remote Similarity	NPC171698
0.6264	Remote Similarity	NPC119633
0.6238	Remote Similarity	NPC323720
0.6237	Remote Similarity	NPC39290
0.6237	Remote Similarity	NPC159369
0.6222	Remote Similarity	NPC477199
0.6207	Remote Similarity	NPC474702
0.6186	Remote Similarity	NPC47076
0.6186	Remote Similarity	NPC134504
0.6184	Remote Similarity	NPC470363
0.6182	Remote Similarity	NPC310467
0.6176	Remote Similarity	NPC475918
0.617	Remote Similarity	NPC477538
0.6163	Remote Similarity	NPC477145
0.6163	Remote Similarity	NPC473741
0.6111	Remote Similarity	NPC137327
0.6091	Remote Similarity	NPC169328
0.6091	Remote Similarity	NPC477237
0.6087	Remote Similarity	NPC289484
0.6087	Remote Similarity	NPC319709
0.6078	Remote Similarity	NPC205176
0.6071	Remote Similarity	NPC263281
0.6071	Remote Similarity	NPC178919
0.6067	Remote Similarity	NPC53858
0.6067	Remote Similarity	NPC84128
0.6053	Remote Similarity	NPC254541
0.6053	Remote Similarity	NPC320598
0.6047	Remote Similarity	NPC330017
0.6038	Remote Similarity	NPC476875
0.6027	Remote Similarity	NPC321118
0.6027	Remote Similarity	NPC316889
0.6	Remote Similarity	NPC322319
0.6	Remote Similarity	NPC326651
0.6	Remote Similarity	NPC476019
0.6	Remote Similarity	NPC325117
0.5982	Remote Similarity	NPC477238
0.5955	Remote Similarity	NPC476302
0.5952	Remote Similarity	NPC55274
0.5952	Remote Similarity	NPC315897
0.5946	Remote Similarity	NPC471917
0.5934	Remote Similarity	NPC472351
0.5929	Remote Similarity	NPC45777
0.5929	Remote Similarity	NPC477061
0.5926	Remote Similarity	NPC471202
0.5926	Remote Similarity	NPC63191
0.5922	Remote Similarity	NPC74035
0.5922	Remote Similarity	NPC14537
0.5921	Remote Similarity	NPC176164
0.5921	Remote Similarity	NPC189301
0.5909	Remote Similarity	NPC469492
0.5909	Remote Similarity	NPC201968
0.59	Remote Similarity	NPC475440
0.5893	Remote Similarity	NPC237420
0.5882	Remote Similarity	NPC477198
0.5875	Remote Similarity	NPC314103
0.5872	Remote Similarity	NPC472536
0.5872	Remote Similarity	NPC103391
0.5865	Remote Similarity	NPC473252
0.5865	Remote Similarity	NPC258130
0.5859	Remote Similarity	NPC475503
0.5859	Remote Similarity	NPC313821
0.5849	Remote Similarity	NPC329305
0.5844	Remote Similarity	NPC321536
0.5843	Remote Similarity	NPC476137
0.5843	Remote Similarity	NPC476156
0.5843	Remote Similarity	NPC469517
0.5843	Remote Similarity	NPC476117
0.5843	Remote Similarity	NPC476243
0.5802	Remote Similarity	NPC238646
0.5802	Remote Similarity	NPC476330
0.58	Remote Similarity	NPC475646
0.5795	Remote Similarity	NPC191774
0.5789	Remote Similarity	NPC292345
0.5783	Remote Similarity	NPC212866
0.5783	Remote Similarity	NPC29598
0.578	Remote Similarity	NPC273814
0.5775	Remote Similarity	NPC180402
0.5775	Remote Similarity	NPC87359
0.5755	Remote Similarity	NPC475150
0.5755	Remote Similarity	NPC15413
0.575	Remote Similarity	NPC474552
0.575	Remote Similarity	NPC316674
0.5747	Remote Similarity	NPC217095
0.5747	Remote Similarity	NPC264417
0.5743	Remote Similarity	NPC234542
0.5743	Remote Similarity	NPC475758
0.5733	Remote Similarity	NPC322573
0.573	Remote Similarity	NPC31756
0.5728	Remote Similarity	NPC227622
0.5728	Remote Similarity	NPC475149
0.5728	Remote Similarity	NPC471097
0.5727	Remote Similarity	NPC50694
0.5714	Remote Similarity	NPC280065
0.5714	Remote Similarity	NPC45060
0.5714	Remote Similarity	NPC313657
0.5714	Remote Similarity	NPC103712
0.5714	Remote Similarity	NPC291196
0.5714	Remote Similarity	NPC36497
0.5714	Remote Similarity	NPC475637
0.5714	Remote Similarity	NPC328447
0.5701	Remote Similarity	NPC473578
0.57	Remote Similarity	NPC189629

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 NPC86064 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	65
0.1-0.2	1851
0.2-0.3	4773
0.3-0.4	1818
0.4-0.5	472
0.5-0.6	150
0.6-0.7	16
0.7-0.8	4
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8194	Intermediate Similarity	NPD3724	Clinical (unspecified phase)
0.7949	Intermediate Similarity	NPD7917	Clinical (unspecified phase)
0.7949	Intermediate Similarity	NPD7918	Clinical (unspecified phase)
0.7432	Intermediate Similarity	NPD2263	Discontinued
0.7349	Intermediate Similarity	NPD7345	Approved
0.7024	Intermediate Similarity	NPD1448	Clinical (unspecified phase)
0.6962	Remote Similarity	NPD3187	Discontinued
0.6962	Remote Similarity	NPD2256	Clinical (unspecified phase)
0.6829	Remote Similarity	NPD2689	Clinical (unspecified phase)
0.6707	Remote Similarity	NPD1453	Phase 1
0.6667	Remote Similarity	NPD8394	Approved
0.6548	Remote Similarity	NPD8144	Approved
0.6548	Remote Similarity	NPD8143	Approved
0.6548	Remote Similarity	NPD3160	Suspended
0.6543	Remote Similarity	NPD6944	Clinical (unspecified phase)
0.6484	Remote Similarity	NPD4264	Clinical (unspecified phase)
0.6429	Remote Similarity	NPD9441	Phase 2
0.6421	Remote Similarity	NPD7844	Discontinued
0.6383	Remote Similarity	NPD5781	Clinical (unspecified phase)
0.6333	Remote Similarity	NPD3723	Clinical (unspecified phase)
0.631	Remote Similarity	NPD2257	Approved
0.6282	Remote Similarity	NPD1831	Phase 3
0.6154	Remote Similarity	NPD8306	Approved
0.6154	Remote Similarity	NPD6413	Approved
0.6154	Remote Similarity	NPD8305	Approved
0.6098	Remote Similarity	NPD2696	Approved
0.6098	Remote Similarity	NPD2695	Approved
0.6098	Remote Similarity	NPD2697	Approved
0.6098	Remote Similarity	NPD2694	Approved
0.6087	Remote Similarity	NPD3211	Approved
0.6064	Remote Similarity	NPD3716	Discontinued
0.6027	Remote Similarity	NPD9419	Clinical (unspecified phase)
0.6022	Remote Similarity	NPD4759	Clinical (unspecified phase)
0.6019	Remote Similarity	NPD7916	Approved
0.6019	Remote Similarity	NPD7915	Approved
0.6	Remote Similarity	NPD8418	Phase 2
0.5972	Remote Similarity	NPD7348	Clinical (unspecified phase)
0.5952	Remote Similarity	NPD1825	Clinical (unspecified phase)
0.5952	Remote Similarity	NPD1147	Phase 2
0.5949	Remote Similarity	NPD364	Discontinued
0.5946	Remote Similarity	NPD1830	Clinical (unspecified phase)
0.5943	Remote Similarity	NPD6421	Discontinued
0.5942	Remote Similarity	NPD1152	Phase 2
0.5938	Remote Similarity	NPD6699	Clinical (unspecified phase)
0.5934	Remote Similarity	NPD3733	Clinical (unspecified phase)
0.5926	Remote Similarity	NPD8298	Phase 2
0.5926	Remote Similarity	NPD5380	Approved
0.5904	Remote Similarity	NPD3726	Approved
0.5904	Remote Similarity	NPD3725	Approved
0.5859	Remote Similarity	NPD3190	Approved
0.5859	Remote Similarity	NPD3191	Approved
0.5859	Remote Similarity	NPD4228	Discovery
0.5859	Remote Similarity	NPD6428	Approved
0.5859	Remote Similarity	NPD3189	Approved
0.5857	Remote Similarity	NPD379	Clinical (unspecified phase)
0.5843	Remote Similarity	NPD5354	Approved
0.5833	Remote Similarity	NPD6094	Approved
0.5833	Remote Similarity	NPD6095	Approved
0.5825	Remote Similarity	NPD8276	Approved
0.5825	Remote Similarity	NPD8275	Approved
0.5824	Remote Similarity	NPD4829	Discontinued
0.581	Remote Similarity	NPD8175	Discontinued
0.5795	Remote Similarity	NPD4278	Clinical (unspecified phase)
0.5789	Remote Similarity	NPD618	Clinical (unspecified phase)
0.5783	Remote Similarity	NPD1815	Discontinued
0.5783	Remote Similarity	NPD7840	Approved
0.5755	Remote Similarity	NPD8174	Phase 2
0.5733	Remote Similarity	NPD3729	Clinical (unspecified phase)
0.5728	Remote Similarity	NPD8085	Approved
0.5728	Remote Similarity	NPD8083	Approved
0.5728	Remote Similarity	NPD8138	Approved
0.5728	Remote Similarity	NPD8086	Approved
0.5728	Remote Similarity	NPD8139	Approved
0.5728	Remote Similarity	NPD8084	Approved
0.5728	Remote Similarity	NPD8082	Approved
0.5714	Remote Similarity	NPD9433	Approved
0.5714	Remote Similarity	NPD9661	Approved
0.5714	Remote Similarity	NPD8277	Approved
0.5714	Remote Similarity	NPD8393	Approved
0.5696	Remote Similarity	NPD574	Approved
0.5679	Remote Similarity	NPD7909	Approved
0.5676	Remote Similarity	NPD3215	Phase 1
0.5673	Remote Similarity	NPD8045	Clinical (unspecified phase)
0.567	Remote Similarity	NPD4780	Clinical (unspecified phase)
0.566	Remote Similarity	NPD8140	Approved
0.566	Remote Similarity	NPD8307	Discontinued
0.5657	Remote Similarity	NPD573	Clinical (unspecified phase)
0.5652	Remote Similarity	NPD7643	Phase 1
0.5644	Remote Similarity	NPD3714	Approved
0.5644	Remote Similarity	NPD3713	Approved
0.5644	Remote Similarity	NPD3715	Approved
0.5638	Remote Similarity	NPD7759	Phase 2
0.5638	Remote Similarity	NPD7760	Phase 2
0.5625	Remote Similarity	NPD9676	Phase 3
0.5625	Remote Similarity	NPD575	Clinical (unspecified phase)
0.5619	Remote Similarity	NPD8081	Approved

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