NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	236.18
Volume:	269.111
LogP:	2.289
LogD:	2.746
LogS:	-3.158
# Rotatable Bonds:	0
TPSA:	40.46
# H-Bond Aceptor:	2
# H-Bond Donor:	2
# Rings:	1
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.635
Synthetic Accessibility Score:	4.787
Fsp3:	0.6
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.468
MDCK Permeability:	2.478755595802795e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.751
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.932
30% Bioavailability (F30%):	0.959

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.688
Plasma Protein Binding (PPB):	76.2000732421875%
Volume Distribution (VD):	1.221
Pgp-substrate:	16.862348556518555%

ADMET: Metabolism

CYP1A2-inhibitor:	0.033
CYP1A2-substrate:	0.181
CYP2C19-inhibitor:	0.03
CYP2C19-substrate:	0.391
CYP2C9-inhibitor:	0.011
CYP2C9-substrate:	0.772
CYP2D6-inhibitor:	0.03
CYP2D6-substrate:	0.854
CYP3A4-inhibitor:	0.011
CYP3A4-substrate:	0.255

ADMET: Excretion

Clearance (CL):	6.33
Half-life (T1/2):	0.748

ADMET: Toxicity

hERG Blockers:	0.027
Human Hepatotoxicity (H-HT):	0.254
Drug-inuced Liver Injury (DILI):	0.071
AMES Toxicity:	0.008
Rat Oral Acute Toxicity:	0.587
Maximum Recommended Daily Dose:	0.982
Skin Sensitization:	0.455
Carcinogencity:	0.856
Eye Corrosion:	0.022
Eye Irritation:	0.786
Respiratory Toxicity:	0.956

Download Data

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

Natural Product: NPC35756

Natural Product ID:	NPC35756
*Common Name:**	2,10,10-Trimethyl-6-Methylene-2,8-Cycloundecadiene-1,5-Diol
IUPAC Name:	(1R,2Z,5S,8E)-2,10,10-trimethyl-6-methylidenecycloundeca-2,8-diene-1,5-diol
Synonyms:
Standard InCHIKey:	QETDLTFNRYOLAT-QULUWVCYSA-N
Standard InCHI:	InChI=1S/C15H24O2/c1-11-6-5-9-15(3,4)10-14(17)12(2)7-8-13(11)16/h5,7,9,13-14,16-17H,1,6,8,10H2,2-4H3/b9-5+,12-7-/t13-,14+/m0/s1
SMILES:	C=C1C/C=C/C(C)(C)C[C@H](/C(=CC[C@@H]1O)/C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL507417
PubChem CID:	10060040
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000129] Alcohols and polyols [CHEMONTID:0001661] Secondary alcohols

*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
NPO7630	Cyperus longus	Species	Cyperaceae	Eukaryota	n.a.	Egyptian herbal medicine	n.a.	PMID[15104485]
NPO7630	Cyperus longus	Species	Cyperaceae	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
IC50	1
Others	4

Activity Type	# Activity
Cell Line	5

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT993	Cell Line	Hepatocyte	Mus musculus	IC50	=	27000.0	nM	PMID[490392]
NPT993	Cell Line	Hepatocyte	Mus musculus	Inhibition	=	80.8	%	PMID[490392]
NPT993	Cell Line	Hepatocyte	Mus musculus	Inhibition	=	47.5	%	PMID[490392]
NPT993	Cell Line	Hepatocyte	Mus musculus	Inhibition	=	25.6	%	PMID[490392]
NPT993	Cell Line	Hepatocyte	Mus musculus	Inhibition	=	11.6	%	PMID[490392]

☑ 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 NPC35756 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	125
0.1-0.2	3254
0.2-0.3	16798
0.3-0.4	13267
0.4-0.5	6590
0.5-0.6	2089
0.6-0.7	434
0.7-0.8	128
0.8-0.85	10
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.8431	Intermediate Similarity	NPC474460
0.8364	Intermediate Similarity	NPC71755
0.8182	Intermediate Similarity	NPC48891
0.8	Intermediate Similarity	NPC329686
0.8	Intermediate Similarity	NPC227135
0.7931	Intermediate Similarity	NPC471081
0.7925	Intermediate Similarity	NPC474495
0.7925	Intermediate Similarity	NPC473672
0.7895	Intermediate Similarity	NPC226848
0.7895	Intermediate Similarity	NPC155025
0.7895	Intermediate Similarity	NPC181872
0.7759	Intermediate Similarity	NPC122239
0.7755	Intermediate Similarity	NPC209279
0.7755	Intermediate Similarity	NPC194586
0.7755	Intermediate Similarity	NPC88079
0.7755	Intermediate Similarity	NPC180871
0.7755	Intermediate Similarity	NPC67761
0.7755	Intermediate Similarity	NPC68889
0.7755	Intermediate Similarity	NPC51758
0.7755	Intermediate Similarity	NPC108494
0.7679	Intermediate Similarity	NPC232247
0.7679	Intermediate Similarity	NPC251666
0.7679	Intermediate Similarity	NPC298299
0.7647	Intermediate Similarity	NPC140501
0.7636	Intermediate Similarity	NPC474496
0.7627	Intermediate Similarity	NPC99487
0.76	Intermediate Similarity	NPC116934
0.7593	Intermediate Similarity	NPC59408
0.7593	Intermediate Similarity	NPC71053
0.7593	Intermediate Similarity	NPC151782
0.7547	Intermediate Similarity	NPC153538
0.7541	Intermediate Similarity	NPC110241
0.75	Intermediate Similarity	NPC15934
0.75	Intermediate Similarity	NPC29091
0.75	Intermediate Similarity	NPC255042
0.75	Intermediate Similarity	NPC182840
0.75	Intermediate Similarity	NPC103213
0.746	Intermediate Similarity	NPC106613
0.7458	Intermediate Similarity	NPC475931
0.7407	Intermediate Similarity	NPC72699
0.7407	Intermediate Similarity	NPC291437
0.7407	Intermediate Similarity	NPC328784
0.7377	Intermediate Similarity	NPC473508
0.7377	Intermediate Similarity	NPC473759
0.7377	Intermediate Similarity	NPC474155
0.7347	Intermediate Similarity	NPC56917
0.7344	Intermediate Similarity	NPC117804
0.7333	Intermediate Similarity	NPC258788
0.7321	Intermediate Similarity	NPC217188
0.7308	Intermediate Similarity	NPC160628
0.7308	Intermediate Similarity	NPC165651
0.7308	Intermediate Similarity	NPC24824
0.7308	Intermediate Similarity	NPC210560
0.7302	Intermediate Similarity	NPC267027
0.7273	Intermediate Similarity	NPC93639
0.7273	Intermediate Similarity	NPC244038
0.7258	Intermediate Similarity	NPC300593
0.7241	Intermediate Similarity	NPC55412
0.7241	Intermediate Similarity	NPC249645
0.7231	Intermediate Similarity	NPC90115
0.7231	Intermediate Similarity	NPC217570
0.7231	Intermediate Similarity	NPC471560
0.7222	Intermediate Similarity	NPC85079
0.7222	Intermediate Similarity	NPC248884
0.7222	Intermediate Similarity	NPC267110
0.7222	Intermediate Similarity	NPC62755
0.7222	Intermediate Similarity	NPC31194
0.7213	Intermediate Similarity	NPC68679
0.7213	Intermediate Similarity	NPC55376
0.7213	Intermediate Similarity	NPC321867
0.7213	Intermediate Similarity	NPC207007
0.72	Intermediate Similarity	NPC269823
0.72	Intermediate Similarity	NPC188596
0.7193	Intermediate Similarity	NPC256209
0.7193	Intermediate Similarity	NPC110732
0.7193	Intermediate Similarity	NPC49059
0.7188	Intermediate Similarity	NPC73603
0.7188	Intermediate Similarity	NPC477791
0.7188	Intermediate Similarity	NPC114651
0.717	Intermediate Similarity	NPC35141
0.717	Intermediate Similarity	NPC124183
0.7143	Intermediate Similarity	NPC19569
0.7143	Intermediate Similarity	NPC68014
0.7143	Intermediate Similarity	NPC308844
0.7143	Intermediate Similarity	NPC187619
0.7121	Intermediate Similarity	NPC286154
0.7121	Intermediate Similarity	NPC189745
0.7115	Intermediate Similarity	NPC138935
0.7097	Intermediate Similarity	NPC83200
0.7091	Intermediate Similarity	NPC288381
0.7091	Intermediate Similarity	NPC20934
0.7091	Intermediate Similarity	NPC182102
0.7091	Intermediate Similarity	NPC26960
0.7077	Intermediate Similarity	NPC167527
0.7077	Intermediate Similarity	NPC471238
0.7069	Intermediate Similarity	NPC281590
0.7069	Intermediate Similarity	NPC317899
0.7069	Intermediate Similarity	NPC148216
0.7069	Intermediate Similarity	NPC474644
0.7069	Intermediate Similarity	NPC130209
0.7069	Intermediate Similarity	NPC148163
0.7059	Intermediate Similarity	NPC46248
0.7059	Intermediate Similarity	NPC213538
0.7059	Intermediate Similarity	NPC304151
0.7059	Intermediate Similarity	NPC256766
0.7059	Intermediate Similarity	NPC249801
0.7049	Intermediate Similarity	NPC240506
0.7049	Intermediate Similarity	NPC66020
0.7031	Intermediate Similarity	NPC250977
0.7031	Intermediate Similarity	NPC311736
0.7031	Intermediate Similarity	NPC326310
0.7015	Intermediate Similarity	NPC477792
0.7015	Intermediate Similarity	NPC95863
0.7015	Intermediate Similarity	NPC474884
0.6984	Remote Similarity	NPC96793
0.6984	Remote Similarity	NPC309300
0.6984	Remote Similarity	NPC323424
0.697	Remote Similarity	NPC473893
0.6964	Remote Similarity	NPC200772
0.6957	Remote Similarity	NPC171148
0.6957	Remote Similarity	NPC313179
0.6957	Remote Similarity	NPC69383
0.6949	Remote Similarity	NPC324224
0.6949	Remote Similarity	NPC474643
0.6949	Remote Similarity	NPC473865
0.6949	Remote Similarity	NPC472808
0.6939	Remote Similarity	NPC34873
0.6939	Remote Similarity	NPC40434
0.6935	Remote Similarity	NPC225342
0.6935	Remote Similarity	NPC260573
0.6935	Remote Similarity	NPC475251
0.6923	Remote Similarity	NPC163290
0.6923	Remote Similarity	NPC269985
0.6923	Remote Similarity	NPC136813
0.6923	Remote Similarity	NPC45782
0.6923	Remote Similarity	NPC82337
0.6912	Remote Similarity	NPC323437
0.6912	Remote Similarity	NPC29542
0.6912	Remote Similarity	NPC201562
0.6912	Remote Similarity	NPC186042
0.6909	Remote Similarity	NPC125122
0.6909	Remote Similarity	NPC471280
0.6909	Remote Similarity	NPC302310
0.6909	Remote Similarity	NPC471275
0.6909	Remote Similarity	NPC471276
0.6897	Remote Similarity	NPC189677
0.6897	Remote Similarity	NPC474127
0.6897	Remote Similarity	NPC473532
0.6875	Remote Similarity	NPC79544
0.6875	Remote Similarity	NPC287339
0.6866	Remote Similarity	NPC34834
0.6852	Remote Similarity	NPC55063
0.6852	Remote Similarity	NPC19834
0.6842	Remote Similarity	NPC142092
0.6833	Remote Similarity	NPC52012
0.6833	Remote Similarity	NPC11130
0.6825	Remote Similarity	NPC124112
0.6818	Remote Similarity	NPC305698
0.6818	Remote Similarity	NPC224532
0.6818	Remote Similarity	NPC96484
0.6812	Remote Similarity	NPC227814
0.6812	Remote Similarity	NPC144995
0.6792	Remote Similarity	NPC101616
0.6786	Remote Similarity	NPC473913
0.6786	Remote Similarity	NPC477727
0.6786	Remote Similarity	NPC249670
0.6786	Remote Similarity	NPC225974
0.6786	Remote Similarity	NPC471281
0.6786	Remote Similarity	NPC474642
0.6786	Remote Similarity	NPC199286
0.678	Remote Similarity	NPC473725
0.678	Remote Similarity	NPC473735
0.678	Remote Similarity	NPC473910
0.678	Remote Similarity	NPC473721
0.678	Remote Similarity	NPC473896
0.678	Remote Similarity	NPC475353
0.678	Remote Similarity	NPC477726
0.678	Remote Similarity	NPC477725
0.6774	Remote Similarity	NPC234264
0.6774	Remote Similarity	NPC469694
0.6774	Remote Similarity	NPC47840
0.6769	Remote Similarity	NPC202017
0.6765	Remote Similarity	NPC471271
0.6765	Remote Similarity	NPC316185
0.6765	Remote Similarity	NPC471662
0.6765	Remote Similarity	NPC471272
0.6765	Remote Similarity	NPC471268
0.6761	Remote Similarity	NPC476007
0.6761	Remote Similarity	NPC91594
0.6731	Remote Similarity	NPC206906
0.6724	Remote Similarity	NPC165755
0.6719	Remote Similarity	NPC107540
0.6719	Remote Similarity	NPC290367
0.6716	Remote Similarity	NPC10758
0.6716	Remote Similarity	NPC250928
0.6716	Remote Similarity	NPC474248
0.6714	Remote Similarity	NPC23231
0.6714	Remote Similarity	NPC60818
0.6714	Remote Similarity	NPC474885
0.6667	Remote Similarity	NPC14352

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 NPC35756 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	124
0.1-0.2	3221
0.2-0.3	4090
0.3-0.4	1402
0.4-0.5	215
0.5-0.6	81
0.6-0.7	12
0.7-0.8	5
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
0.7647	Intermediate Similarity	NPD4265	Approved
0.7241	Intermediate Similarity	NPD4219	Approved
0.7213	Intermediate Similarity	NPD368	Approved
0.7164	Intermediate Similarity	NPD4732	Discontinued
0.7069	Intermediate Similarity	NPD342	Phase 1
0.6957	Remote Similarity	NPD8264	Approved
0.6721	Remote Similarity	NPD585	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD7322	Clinical (unspecified phase)
0.6508	Remote Similarity	NPD4246	Clinical (unspecified phase)
0.6486	Remote Similarity	NPD7514	Phase 3
0.6486	Remote Similarity	NPD7332	Phase 2
0.6438	Remote Similarity	NPD7145	Approved
0.64	Remote Similarity	NPD6902	Approved
0.6377	Remote Similarity	NPD7143	Approved
0.6377	Remote Similarity	NPD7144	Approved
0.6308	Remote Similarity	NPD3210	Clinical (unspecified phase)
0.6301	Remote Similarity	NPD6925	Approved
0.6301	Remote Similarity	NPD5776	Phase 2
0.6286	Remote Similarity	NPD7151	Approved
0.6286	Remote Similarity	NPD7150	Approved
0.6286	Remote Similarity	NPD7152	Approved
0.6232	Remote Similarity	NPD6922	Approved
0.6232	Remote Similarity	NPD6923	Approved
0.6216	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.6176	Remote Similarity	NPD4247	Clinical (unspecified phase)
0.6154	Remote Similarity	NPD4192	Approved
0.6154	Remote Similarity	NPD4193	Approved
0.6154	Remote Similarity	NPD4191	Approved
0.6154	Remote Similarity	NPD4194	Approved
0.6133	Remote Similarity	NPD6929	Approved
0.6111	Remote Similarity	NPD6926	Approved
0.6111	Remote Similarity	NPD6924	Approved
0.6081	Remote Similarity	NPD6932	Approved
0.6053	Remote Similarity	NPD6931	Approved
0.6053	Remote Similarity	NPD6930	Phase 2
0.6034	Remote Similarity	NPD4220	Pre-registration
0.6	Remote Similarity	NPD4268	Approved
0.6	Remote Similarity	NPD4271	Approved
0.5974	Remote Similarity	NPD6898	Phase 1
0.5949	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.5946	Remote Similarity	NPD3701	Clinical (unspecified phase)
0.5946	Remote Similarity	NPD6933	Approved
0.5844	Remote Similarity	NPD8259	Clinical (unspecified phase)
0.5844	Remote Similarity	NPD4820	Approved
0.5844	Remote Similarity	NPD4822	Approved
0.5844	Remote Similarity	NPD4821	Approved
0.5844	Remote Similarity	NPD4252	Approved
0.5844	Remote Similarity	NPD4819	Approved
0.5844	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.5823	Remote Similarity	NPD5331	Approved
0.5823	Remote Similarity	NPD5362	Discontinued
0.5823	Remote Similarity	NPD6695	Phase 3
0.5823	Remote Similarity	NPD5332	Approved
0.5823	Remote Similarity	NPD7154	Phase 3
0.5811	Remote Similarity	NPD7339	Approved
0.5811	Remote Similarity	NPD6942	Approved
0.5789	Remote Similarity	NPD39	Approved
0.5769	Remote Similarity	NPD4790	Discontinued
0.575	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.5735	Remote Similarity	NPD277	Approved
0.5735	Remote Similarity	NPD5325	Clinical (unspecified phase)
0.5732	Remote Similarity	NPD4751	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD6683	Phase 2
0.5696	Remote Similarity	NPD4269	Approved
0.5696	Remote Similarity	NPD4270	Approved
0.5694	Remote Similarity	NPD3212	Clinical (unspecified phase)
0.5679	Remote Similarity	NPD6893	Approved
0.5667	Remote Similarity	NPD2268	Discontinued
0.5652	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.5647	Remote Similarity	NPD7637	Suspended
0.5641	Remote Similarity	NPD7509	Discontinued

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