NPASS Compound

Structure

CID225103 OpenBabel06191716022D 41 44 0 0 1 0 0 0 0 0999 V2000 -0.5924 1.6276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5924 -2.0261 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4187 1.9284 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5603 0.5240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8642 -0.5104 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5222 -1.4501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6428 -0.7660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2470 -2.1840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3809 -2.6840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2470 -1.1840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5149 -2.1840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3809 -0.6840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6489 -0.6840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7829 -1.1840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1848 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5924 0.3420 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1736 -0.9848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7660 0.6428 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5924 -1.0261 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5209 2.2704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0603 1.3900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5149 -1.1840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1133 -1.3268 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1848 -0.6840 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.9168 -0.6840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.6840 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7057 0.3008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4397 -1.2080 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1133 0.6428 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4397 0.5240 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8794 -0.6840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6946 3.2552 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5603 2.2561 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9397 0.3420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9168 0.3160 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0603 -2.0741 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2870 1.6276 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0603 1.3900 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0508 -1.1840 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 18 1 0 0 0 0 2 19 2 0 0 0 0 3 20 1 0 0 0 0 4 21 1 0 0 0 0 5 32 1 0 0 0 0 6 32 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 9 11 1 0 0 0 0 10 12 2 0 0 0 0 11 22 2 0 0 0 0 12 22 1 0 0 0 0 13 14 2 0 0 0 0 13 22 1 0 0 0 0 14 26 1 0 0 0 0 15 16 1 0 0 0 0 15 25 1 0 0 0 0 16 33 1 0 0 0 0 17 24 1 0 0 0 0 18 24 1 0 0 0 0 18 28 2 0 0 0 0 19 25 1 0 0 0 0 19 27 1 0 0 0 0 20 34 2 0 0 0 0 20 39 1 0 0 0 0 21 35 2 0 0 0 0 21 40 1 0 0 0 0 23 17 1 6 0 0 0 23 29 1 0 0 0 0 23 32 1 0 0 0 0 24 36 2 0 0 0 0 25 41 1 6 0 0 0 26 37 2 0 0 0 0 26 41 1 0 0 0 0 27 29 1 0 0 0 0 27 33 1 1 0 0 0 28 30 1 0 0 0 0 28 32 1 0 0 0 0 29 38 1 6 0 0 0 30 31 1 0 0 0 0 30 39 1 1 0 0 0 31 33 1 6 0 0 0 31 40 1 0 0 0 0 33 7 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	564.27
Volume:	589.055
LogP:	4.132
LogD:	3.406
LogS:	-4.928
# Rotatable Bonds:	8
TPSA:	116.2
# H-Bond Aceptor:	8
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.236
Synthetic Accessibility Score:	5.456
Fsp3:	0.515
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.894
MDCK Permeability:	5.136966137797572e-05
Pgp-inhibitor:	0.996
Pgp-substrate:	0.498
Human Intestinal Absorption (HIA):	0.015
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.55

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.467
Plasma Protein Binding (PPB):	81.59412384033203%
Volume Distribution (VD):	1.474
Pgp-substrate:	16.35471534729004%

ADMET: Metabolism

CYP1A2-inhibitor:	0.221
CYP1A2-substrate:	0.053
CYP2C19-inhibitor:	0.585
CYP2C19-substrate:	0.081
CYP2C9-inhibitor:	0.898
CYP2C9-substrate:	0.089
CYP2D6-inhibitor:	0.633
CYP2D6-substrate:	0.072
CYP3A4-inhibitor:	0.778
CYP3A4-substrate:	0.43

ADMET: Excretion

Clearance (CL):	3.217
Half-life (T1/2):	0.031

ADMET: Toxicity

hERG Blockers:	0.03
Human Hepatotoxicity (H-HT):	0.536
Drug-inuced Liver Injury (DILI):	0.923
AMES Toxicity:	0.07
Rat Oral Acute Toxicity:	0.67
Maximum Recommended Daily Dose:	0.906
Skin Sensitization:	0.107
Carcinogencity:	0.162
Eye Corrosion:	0.006
Eye Irritation:	0.026
Respiratory Toxicity:	0.964

Download Data

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

Natural Product: NPC225103

Natural Product ID:	NPC225103
*Common Name:**	SPZFWGXRAFVTPQ-ZQXBODBKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SPZFWGXRAFVTPQ-ZQXBODBKSA-N
Standard InCHI:	InChI=1S/C33H40O8/c1-18-24(36)17-23-29(38)27-19(2)25(41-26(37)14-13-22-11-9-8-10-12-22)15-16-33(27,7)31(40-21(4)35)30(39-20(3)34)28(18)32(23,5)6/h8-14,23,25,27,29-31,38H,2,15-17H2,1,3-7H3/b14-13+/t23-,25-,27-,29+,30+,31-,33+/m0/s1
SMILES:	CC(=O)O[C@H]1[C@H](OC(=O)C)C2=C(C)C(=O)C[C@H](C2(C)C)[C@H]([C@H]2[C@@]1(C)CC[C@@H](C2=C)OC(=O)/C=C/c1ccccc1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL454520
PubChem CID:	10698187
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0000676] Taxanes and derivatives

*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
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	Japan	n.a.	PMID[14987066]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15844936]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15974623]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	Japan	n.a.	PMID[15974623]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23265441]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7561894]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7908950]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24820	Taxus cuspidata	Species	Taxaceae	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

Activity Type	# Activity
Others	1

Activity Type	# Activity
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		Activity	=	191.0	%	PMID[573445]

☑ 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 NPC225103 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	246
0.1-0.2	880
0.2-0.3	2062
0.3-0.4	4638
0.4-0.5	8222
0.5-0.6	17185
0.6-0.7	8378
0.7-0.8	1007
0.8-0.85	50
0.85-0.9	13
0.9-0.95	10
0.95-1	6

Similarity Score	Similarity Level	Natural Product ID
0.9918	High Similarity	NPC473443
0.9918	High Similarity	NPC472388
0.96	High Similarity	NPC80599
0.96	High Similarity	NPC209851
0.9587	High Similarity	NPC469742
0.9435	High Similarity	NPC195224
0.9355	High Similarity	NPC473423
0.9344	High Similarity	NPC12016
0.9268	High Similarity	NPC472373
0.9213	High Similarity	NPC472361
0.9213	High Similarity	NPC472418
0.9194	High Similarity	NPC471758
0.9154	High Similarity	NPC472374
0.9154	High Similarity	NPC472372
0.9141	High Similarity	NPC472394
0.912	High Similarity	NPC45821
0.907	High Similarity	NPC472437
0.8992	High Similarity	NPC475493
0.8992	High Similarity	NPC471880
0.8934	High Similarity	NPC89324
0.8871	High Similarity	NPC473439
0.8871	High Similarity	NPC300827
0.8815	High Similarity	NPC34012
0.8806	High Similarity	NPC473440
0.88	High Similarity	NPC473749
0.876	High Similarity	NPC93632
0.8759	High Similarity	NPC301946
0.8759	High Similarity	NPC277053
0.8731	High Similarity	NPC472395
0.8731	High Similarity	NPC472371
0.8686	High Similarity	NPC471912
0.8686	High Similarity	NPC80895
0.8657	High Similarity	NPC184109
0.8633	High Similarity	NPC217918
0.8618	High Similarity	NPC470820
0.8605	High Similarity	NPC190849
0.8605	High Similarity	NPC171007
0.8571	High Similarity	NPC471911
0.8571	High Similarity	NPC4242
0.8551	High Similarity	NPC38696
0.854	High Similarity	NPC63737
0.8529	High Similarity	NPC472547
0.8529	High Similarity	NPC475400
0.8516	High Similarity	NPC140118
0.8516	High Similarity	NPC12881
0.8511	High Similarity	NPC91730
0.8507	High Similarity	NPC477893
0.8504	High Similarity	NPC475328
0.8496	Intermediate Similarity	NPC15850
0.8451	Intermediate Similarity	NPC197037
0.8429	Intermediate Similarity	NPC474935
0.8417	Intermediate Similarity	NPC111466
0.8406	Intermediate Similarity	NPC140021
0.8397	Intermediate Similarity	NPC230331
0.8394	Intermediate Similarity	NPC90614
0.8385	Intermediate Similarity	NPC470816
0.8385	Intermediate Similarity	NPC473082
0.8385	Intermediate Similarity	NPC470818
0.8382	Intermediate Similarity	NPC39549
0.837	Intermediate Similarity	NPC477896
0.8357	Intermediate Similarity	NPC264270
0.8357	Intermediate Similarity	NPC40085
0.8345	Intermediate Similarity	NPC477894
0.8333	Intermediate Similarity	NPC27377
0.8333	Intermediate Similarity	NPC87448
0.8333	Intermediate Similarity	NPC97947
0.8333	Intermediate Similarity	NPC291599
0.8333	Intermediate Similarity	NPC134685
0.8333	Intermediate Similarity	NPC41481
0.8333	Intermediate Similarity	NPC16912
0.8333	Intermediate Similarity	NPC248265
0.8333	Intermediate Similarity	NPC472576
0.8333	Intermediate Similarity	NPC219419
0.8333	Intermediate Similarity	NPC118080
0.8333	Intermediate Similarity	NPC11588
0.8333	Intermediate Similarity	NPC229545
0.8321	Intermediate Similarity	NPC476971
0.8321	Intermediate Similarity	NPC169913
0.8321	Intermediate Similarity	NPC476972
0.8309	Intermediate Similarity	NPC472545
0.8309	Intermediate Similarity	NPC472551
0.8308	Intermediate Similarity	NPC473083
0.8296	Intermediate Similarity	NPC203486
0.8296	Intermediate Similarity	NPC48929
0.8284	Intermediate Similarity	NPC476976
0.8276	Intermediate Similarity	NPC114357
0.8276	Intermediate Similarity	NPC259144
0.8276	Intermediate Similarity	NPC21410
0.8276	Intermediate Similarity	NPC473670
0.8276	Intermediate Similarity	NPC155329
0.8273	Intermediate Similarity	NPC472546
0.8273	Intermediate Similarity	NPC182869
0.8271	Intermediate Similarity	NPC475138
0.8261	Intermediate Similarity	NPC100913
0.8261	Intermediate Similarity	NPC171207
0.8261	Intermediate Similarity	NPC275592
0.8261	Intermediate Similarity	NPC97667
0.8252	Intermediate Similarity	NPC7095
0.8244	Intermediate Similarity	NPC275576
0.8244	Intermediate Similarity	NPC475933
0.8244	Intermediate Similarity	NPC470158
0.8244	Intermediate Similarity	NPC476970
0.824	Intermediate Similarity	NPC476476
0.8231	Intermediate Similarity	NPC470815
0.8227	Intermediate Similarity	NPC476973
0.8227	Intermediate Similarity	NPC174982
0.8227	Intermediate Similarity	NPC472572
0.8227	Intermediate Similarity	NPC470159
0.8227	Intermediate Similarity	NPC473088
0.8227	Intermediate Similarity	NPC471104
0.8227	Intermediate Similarity	NPC472571
0.8227	Intermediate Similarity	NPC29704
0.8227	Intermediate Similarity	NPC127857
0.8227	Intermediate Similarity	NPC96903
0.8227	Intermediate Similarity	NPC472575
0.8227	Intermediate Similarity	NPC472556
0.8227	Intermediate Similarity	NPC70403
0.8227	Intermediate Similarity	NPC470157
0.8227	Intermediate Similarity	NPC177940
0.8227	Intermediate Similarity	NPC200471
0.8227	Intermediate Similarity	NPC472568
0.8227	Intermediate Similarity	NPC171525
0.8227	Intermediate Similarity	NPC469349
0.8227	Intermediate Similarity	NPC184817
0.8227	Intermediate Similarity	NPC158663
0.8227	Intermediate Similarity	NPC473541
0.8214	Intermediate Similarity	NPC95449
0.8214	Intermediate Similarity	NPC163087
0.8209	Intermediate Similarity	NPC476977
0.8201	Intermediate Similarity	NPC224491
0.8182	Intermediate Similarity	NPC81698
0.8182	Intermediate Similarity	NPC250046
0.8182	Intermediate Similarity	NPC60509
0.8169	Intermediate Similarity	NPC473602
0.8169	Intermediate Similarity	NPC94602
0.8168	Intermediate Similarity	NPC284022
0.8156	Intermediate Similarity	NPC472569
0.8156	Intermediate Similarity	NPC70716
0.8156	Intermediate Similarity	NPC472573
0.8156	Intermediate Similarity	NPC95810
0.8156	Intermediate Similarity	NPC125106
0.8156	Intermediate Similarity	NPC241951
0.8156	Intermediate Similarity	NPC470152
0.8156	Intermediate Similarity	NPC57628
0.8156	Intermediate Similarity	NPC476974
0.8156	Intermediate Similarity	NPC472570
0.8156	Intermediate Similarity	NPC11685
0.8156	Intermediate Similarity	NPC163719
0.8156	Intermediate Similarity	NPC475122
0.8156	Intermediate Similarity	NPC475759
0.8156	Intermediate Similarity	NPC95265
0.8156	Intermediate Similarity	NPC188865
0.8156	Intermediate Similarity	NPC25768
0.8143	Intermediate Similarity	NPC473755
0.8143	Intermediate Similarity	NPC475135
0.8143	Intermediate Similarity	NPC475513
0.8143	Intermediate Similarity	NPC192658
0.8138	Intermediate Similarity	NPC472548
0.8129	Intermediate Similarity	NPC87934
0.8129	Intermediate Similarity	NPC162613
0.8129	Intermediate Similarity	NPC477904
0.8129	Intermediate Similarity	NPC183270
0.8125	Intermediate Similarity	NPC161239
0.8125	Intermediate Similarity	NPC470245
0.8125	Intermediate Similarity	NPC198455
0.8125	Intermediate Similarity	NPC473214
0.8125	Intermediate Similarity	NPC112216
0.8125	Intermediate Similarity	NPC165260
0.812	Intermediate Similarity	NPC58061
0.811	Intermediate Similarity	NPC152812
0.8102	Intermediate Similarity	NPC473399
0.8102	Intermediate Similarity	NPC471864
0.8102	Intermediate Similarity	NPC291638
0.8102	Intermediate Similarity	NPC472577
0.8102	Intermediate Similarity	NPC473216
0.8102	Intermediate Similarity	NPC66761
0.8102	Intermediate Similarity	NPC195647
0.8102	Intermediate Similarity	NPC17877
0.8095	Intermediate Similarity	NPC217091
0.8092	Intermediate Similarity	NPC307139
0.8085	Intermediate Similarity	NPC477468
0.8082	Intermediate Similarity	NPC256142
0.8082	Intermediate Similarity	NPC242262
0.8082	Intermediate Similarity	NPC265395
0.8082	Intermediate Similarity	NPC472005
0.8082	Intermediate Similarity	NPC473414
0.8082	Intermediate Similarity	NPC249471
0.8082	Intermediate Similarity	NPC237549
0.8082	Intermediate Similarity	NPC304876
0.8082	Intermediate Similarity	NPC472030
0.8082	Intermediate Similarity	NPC472022
0.8082	Intermediate Similarity	NPC1173
0.8082	Intermediate Similarity	NPC257213
0.8082	Intermediate Similarity	NPC158333
0.8077	Intermediate Similarity	NPC70973
0.8071	Intermediate Similarity	NPC266374
0.8069	Intermediate Similarity	NPC101043
0.8069	Intermediate Similarity	NPC306799
0.8069	Intermediate Similarity	NPC51602
0.8069	Intermediate Similarity	NPC471103

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 NPC225103 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	218
0.1-0.2	681
0.2-0.3	1418
0.3-0.4	2853
0.4-0.5	2258
0.5-0.6	1412
0.6-0.7	292
0.7-0.8	18
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
0.7698	Intermediate Similarity	NPD7966	Clinical (unspecified phase)
0.7603	Intermediate Similarity	NPD7236	Approved
0.7597	Intermediate Similarity	NPD2629	Approved
0.7586	Intermediate Similarity	NPD8166	Discontinued
0.7578	Intermediate Similarity	NPD6858	Approved
0.7578	Intermediate Similarity	NPD7094	Approved
0.7516	Intermediate Similarity	NPD8368	Discontinued
0.75	Intermediate Similarity	NPD7961	Discontinued
0.7482	Intermediate Similarity	NPD5952	Clinical (unspecified phase)
0.7467	Intermediate Similarity	NPD7239	Suspended
0.7438	Intermediate Similarity	NPD8470	Clinical (unspecified phase)
0.7419	Intermediate Similarity	NPD6647	Phase 2
0.7378	Intermediate Similarity	NPD8407	Phase 2
0.7375	Intermediate Similarity	NPD7799	Discontinued
0.7289	Intermediate Similarity	NPD8424	Clinical (unspecified phase)
0.7289	Intermediate Similarity	NPD8434	Phase 2
0.7287	Intermediate Similarity	NPD4141	Clinical (unspecified phase)
0.7278	Intermediate Similarity	NPD8127	Discontinued
0.7273	Intermediate Similarity	NPD4198	Discontinued
0.7252	Intermediate Similarity	NPD6010	Discontinued
0.7241	Intermediate Similarity	NPD7305	Phase 1
0.723	Intermediate Similarity	NPD4628	Phase 3
0.7222	Intermediate Similarity	NPD5909	Discontinued
0.7209	Intermediate Similarity	NPD2067	Discontinued
0.7206	Intermediate Similarity	NPD7457	Clinical (unspecified phase)
0.7202	Intermediate Similarity	NPD8361	Approved
0.7202	Intermediate Similarity	NPD8360	Approved
0.7202	Intermediate Similarity	NPD8435	Approved
0.719	Intermediate Similarity	NPD5122	Clinical (unspecified phase)
0.7177	Intermediate Similarity	NPD2066	Phase 3
0.7143	Intermediate Similarity	NPD6007	Clinical (unspecified phase)
0.7132	Intermediate Similarity	NPD3412	Clinical (unspecified phase)
0.7132	Intermediate Similarity	NPD6831	Clinical (unspecified phase)
0.7113	Intermediate Similarity	NPD7008	Discontinued
0.7111	Intermediate Similarity	NPD7741	Discontinued
0.7109	Intermediate Similarity	NPD6685	Approved
0.7068	Intermediate Similarity	NPD5951	Approved
0.7067	Intermediate Similarity	NPD7274	Clinical (unspecified phase)
0.704	Intermediate Similarity	NPD7798	Approved
0.7031	Intermediate Similarity	NPD5048	Discontinued
0.7025	Intermediate Similarity	NPD7058	Phase 2
0.7025	Intermediate Similarity	NPD7057	Phase 3
0.7023	Intermediate Similarity	NPD2181	Clinical (unspecified phase)
0.7014	Intermediate Similarity	NPD6663	Approved
0.7008	Intermediate Similarity	NPD1931	Clinical (unspecified phase)
0.7008	Intermediate Similarity	NPD1929	Approved
0.7008	Intermediate Similarity	NPD1930	Approved
0.7007	Intermediate Similarity	NPD5126	Approved
0.7007	Intermediate Similarity	NPD5125	Phase 3
0.7	Intermediate Similarity	NPD2182	Approved
0.6972	Remote Similarity	NPD5736	Approved
0.6954	Remote Similarity	NPD8485	Approved
0.6954	Remote Similarity	NPD6190	Approved
0.6913	Remote Similarity	NPD7702	Clinical (unspecified phase)
0.6912	Remote Similarity	NPD7610	Discontinued
0.6887	Remote Similarity	NPD6398	Clinical (unspecified phase)
0.6884	Remote Similarity	NPD7163	Clinical (unspecified phase)
0.6883	Remote Similarity	NPD6273	Approved
0.6875	Remote Similarity	NPD5765	Approved
0.6857	Remote Similarity	NPD6637	Approved
0.6842	Remote Similarity	NPD6912	Phase 3
0.6836	Remote Similarity	NPD8486	Clinical (unspecified phase)
0.6835	Remote Similarity	NPD37	Approved
0.6828	Remote Similarity	NPD3764	Approved
0.6813	Remote Similarity	NPD4966	Approved
0.6813	Remote Similarity	NPD4965	Approved
0.6813	Remote Similarity	NPD4967	Phase 2
0.68	Remote Similarity	NPD7266	Discontinued
0.6797	Remote Similarity	NPD1932	Approved
0.6794	Remote Similarity	NPD6686	Approved
0.6792	Remote Similarity	NPD7819	Suspended
0.6786	Remote Similarity	NPD6287	Discontinued
0.6784	Remote Similarity	NPD8150	Discontinued
0.6783	Remote Similarity	NPD5740	Clinical (unspecified phase)
0.6783	Remote Similarity	NPD6085	Phase 2
0.6781	Remote Similarity	NPD8032	Phase 2
0.6765	Remote Similarity	NPD7115	Discovery
0.6763	Remote Similarity	NPD2932	Approved
0.6752	Remote Similarity	NPD6591	Clinical (unspecified phase)
0.6752	Remote Similarity	NPD7458	Discontinued
0.6744	Remote Similarity	NPD5738	Clinical (unspecified phase)
0.6742	Remote Similarity	NPD2329	Discontinued
0.6725	Remote Similarity	NPD8055	Clinical (unspecified phase)
0.671	Remote Similarity	NPD8389	Clinical (unspecified phase)
0.6706	Remote Similarity	NPD8312	Approved
0.6706	Remote Similarity	NPD8313	Approved
0.6694	Remote Similarity	NPD1088	Approved
0.6693	Remote Similarity	NPD7638	Approved
0.6692	Remote Similarity	NPD164	Approved
0.6691	Remote Similarity	NPD690	Clinical (unspecified phase)
0.669	Remote Similarity	NPD7055	Discontinued
0.6689	Remote Similarity	NPD6355	Discontinued
0.6689	Remote Similarity	NPD2346	Discontinued
0.6667	Remote Similarity	NPD7714	Approved
0.6667	Remote Similarity	NPD4109	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD1989	Approved
0.6667	Remote Similarity	NPD4110	Phase 3
0.6667	Remote Similarity	NPD7715	Approved
0.6646	Remote Similarity	NPD3226	Approved
0.6643	Remote Similarity	NPD3019	Approved
0.6642	Remote Similarity	NPD3317	Approved
0.6641	Remote Similarity	NPD7640	Approved
0.6641	Remote Similarity	NPD7639	Approved
0.6626	Remote Similarity	NPD6234	Discontinued
0.6623	Remote Similarity	NPD2438	Suspended
0.6622	Remote Similarity	NPD4140	Approved
0.6621	Remote Similarity	NPD7084	Phase 3
0.6619	Remote Similarity	NPD7009	Phase 2
0.6614	Remote Similarity	NPD3495	Discontinued
0.6614	Remote Similarity	NPD7902	Approved
0.6609	Remote Similarity	NPD8397	Clinical (unspecified phase)
0.6603	Remote Similarity	NPD7004	Clinical (unspecified phase)
0.6601	Remote Similarity	NPD7421	Clinical (unspecified phase)
0.66	Remote Similarity	NPD7097	Phase 1
0.6593	Remote Similarity	NPD1609	Clinical (unspecified phase)
0.6593	Remote Similarity	NPD8297	Approved
0.6588	Remote Similarity	NPD6764	Approved
0.6588	Remote Similarity	NPD6765	Approved
0.6587	Remote Similarity	NPD1693	Approved
0.6587	Remote Similarity	NPD7473	Discontinued
0.6584	Remote Similarity	NPD7096	Clinical (unspecified phase)
0.6584	Remote Similarity	NPD8455	Phase 2
0.6579	Remote Similarity	NPD5762	Approved
0.6579	Remote Similarity	NPD5763	Approved
0.6567	Remote Similarity	NPD5955	Clinical (unspecified phase)
0.6565	Remote Similarity	NPD1237	Approved
0.6564	Remote Similarity	NPD7075	Discontinued
0.6558	Remote Similarity	NPD7003	Approved
0.6556	Remote Similarity	NPD2799	Discontinued
0.6549	Remote Similarity	NPD4807	Approved
0.6549	Remote Similarity	NPD4806	Approved
0.6548	Remote Similarity	NPD7228	Approved
0.6547	Remote Similarity	NPD6065	Approved
0.6534	Remote Similarity	NPD7879	Clinical (unspecified phase)
0.6532	Remote Similarity	NPD1089	Approved
0.6532	Remote Similarity	NPD3672	Approved
0.6532	Remote Similarity	NPD1086	Approved
0.6532	Remote Similarity	NPD3673	Approved
0.6532	Remote Similarity	NPD1090	Approved
0.6531	Remote Similarity	NPD7095	Approved
0.6528	Remote Similarity	NPD1283	Approved
0.6525	Remote Similarity	NPD5305	Approved
0.6525	Remote Similarity	NPD5306	Approved
0.6512	Remote Similarity	NPD1238	Approved
0.651	Remote Similarity	NPD2979	Phase 3
0.6509	Remote Similarity	NPD5844	Phase 1
0.6508	Remote Similarity	NPD7748	Approved
0.6503	Remote Similarity	NPD1608	Approved
0.65	Remote Similarity	NPD4380	Phase 2
0.65	Remote Similarity	NPD6599	Discontinued
0.65	Remote Similarity	NPD7028	Phase 2
0.65	Remote Similarity	NPD9545	Approved
0.6493	Remote Similarity	NPD4061	Clinical (unspecified phase)
0.6486	Remote Similarity	NPD6798	Discontinued
0.6486	Remote Similarity	NPD2313	Discontinued
0.6479	Remote Similarity	NPD3026	Approved
0.6479	Remote Similarity	NPD3023	Approved
0.6471	Remote Similarity	NPD6004	Phase 3
0.6471	Remote Similarity	NPD6005	Phase 3
0.6471	Remote Similarity	NPD6006	Clinical (unspecified phase)
0.6471	Remote Similarity	NPD2343	Clinical (unspecified phase)
0.6471	Remote Similarity	NPD6002	Phase 3
0.6471	Remote Similarity	NPD6003	Clinical (unspecified phase)
0.6457	Remote Similarity	NPD688	Clinical (unspecified phase)
0.6457	Remote Similarity	NPD6048	Clinical (unspecified phase)
0.6457	Remote Similarity	NPD6049	Phase 2
0.6454	Remote Similarity	NPD3024	Approved
0.6454	Remote Similarity	NPD3025	Approved
0.6452	Remote Similarity	NPD3750	Approved
0.6452	Remote Similarity	NPD5347	Phase 2
0.6452	Remote Similarity	NPD5346	Phase 2
0.6452	Remote Similarity	NPD800	Approved
0.6444	Remote Similarity	NPD1317	Discontinued
0.6443	Remote Similarity	NPD7713	Phase 3
0.6443	Remote Similarity	NPD6233	Phase 2
0.6442	Remote Similarity	NPD5402	Approved
0.6438	Remote Similarity	NPD5808	Clinical (unspecified phase)
0.6437	Remote Similarity	NPD6785	Approved
0.6437	Remote Similarity	NPD6784	Approved
0.6436	Remote Similarity	NPD8462	Phase 1
0.6434	Remote Similarity	NPD5926	Approved
0.6434	Remote Similarity	NPD9495	Approved
0.6434	Remote Similarity	NPD4225	Approved
0.6434	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.6433	Remote Similarity	NPD6143	Clinical (unspecified phase)
0.6429	Remote Similarity	NPD7631	Approved
0.6429	Remote Similarity	NPD6399	Phase 3
0.6424	Remote Similarity	NPD5537	Clinical (unspecified phase)
0.6423	Remote Similarity	NPD4632	Approved
0.642	Remote Similarity	NPD6801	Discontinued
0.6414	Remote Similarity	NPD8651	Approved
0.6407	Remote Similarity	NPD6232	Discontinued
0.6405	Remote Similarity	NPD6099	Approved
0.6405	Remote Similarity	NPD6100	Approved
0.6402	Remote Similarity	NPD4868	Clinical (unspecified phase)
0.64	Remote Similarity	NPD7838	Discovery
0.6397	Remote Similarity	NPD6649	Approved
0.6397	Remote Similarity	NPD6650	Approved
0.6395	Remote Similarity	NPD7240	Approved
0.6395	Remote Similarity	NPD7685	Pre-registration

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