Structure

Physi-Chem Properties

Molecular Weight:  238.19
Volume:  265.827
LogP:  3.347
LogD:  3.773
LogS:  -3.416
# Rotatable Bonds:  0
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.637
Synthetic Accessibility Score:  4.594
Fsp3:  0.867
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.496
MDCK Permeability:  2.497846980986651e-05
Pgp-inhibitor:  0.904
Pgp-substrate:  0.929
Human Intestinal Absorption (HIA):  0.023
20% Bioavailability (F20%):  0.951
30% Bioavailability (F30%):  0.953

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.915
Plasma Protein Binding (PPB):  83.2890396118164%
Volume Distribution (VD):  0.944
Pgp-substrate:  27.12244415283203%

ADMET: Metabolism

CYP1A2-inhibitor:  0.048
CYP1A2-substrate:  0.107
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.621
CYP2C9-inhibitor:  0.034
CYP2C9-substrate:  0.456
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.436
CYP3A4-inhibitor:  0.026
CYP3A4-substrate:  0.198

ADMET: Excretion

Clearance (CL):  10.903
Half-life (T1/2):  0.61

ADMET: Toxicity

hERG Blockers:  0.049
Human Hepatotoxicity (H-HT):  0.19
Drug-inuced Liver Injury (DILI):  0.032
AMES Toxicity:  0.006
Rat Oral Acute Toxicity:  0.921
Maximum Recommended Daily Dose:  0.936
Skin Sensitization:  0.88
Carcinogencity:  0.253
Eye Corrosion:  0.417
Eye Irritation:  0.582
Respiratory Toxicity:  0.968

Download Data

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

  Natural Product: NPC61503

Natural Product ID:  NPC61503
Common Name*:   1,5,8,8-Tetramethyl-8-Bicyclo[8.1.0]Undecene-2,9-Diol
IUPAC Name:   (1S,2S,5E,9S,10R)-3,3,6,10-tetramethylbicyclo[8.1.0]undec-5-ene-2,9-diol
Synonyms:  
Standard InCHIKey:  RKDPETZBSSPSSM-SSHMBCCFSA-N
Standard InCHI:  InChI=1S/C15H26O2/c1-10-5-6-12(16)15(4)9-11(15)13(17)14(2,3)8-7-10/h7,11-13,16-17H,5-6,8-9H2,1-4H3/b10-7+/t11-,12+,13+,15-/m1/s1
SMILES:  C/C/1=CCC(C)(C)[C@H]([C@H]2C[C@@]2(C)[C@H](CC1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL450757
PubChem CID:   10331790
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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT993 Cell Line Hepatocyte Mus musculus IC50 = 70000.0 nM PMID[449334]
NPT993 Cell Line Hepatocyte Mus musculus Inhibition = 54.8 % PMID[449334]
NPT993 Cell Line Hepatocyte Mus musculus Inhibition = 37.3 % PMID[449334]
NPT993 Cell Line Hepatocyte Mus musculus Inhibition = 16.6 % PMID[449334]
NPT993 Cell Line Hepatocyte Mus musculus Inhibition = 5.9 % PMID[449334]

☑ 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 NPC61503 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.8438 Intermediate Similarity NPC473508
0.8333 Intermediate Similarity NPC311736
0.8308 Intermediate Similarity NPC300593
0.8209 Intermediate Similarity NPC163290
0.8182 Intermediate Similarity NPC471200
0.8125 Intermediate Similarity NPC99487
0.8028 Intermediate Similarity NPC190859
0.8 Intermediate Similarity NPC225342
0.7879 Intermediate Similarity NPC211291
0.7879 Intermediate Similarity NPC133368
0.7812 Intermediate Similarity NPC155025
0.7808 Intermediate Similarity NPC268111
0.7808 Intermediate Similarity NPC170148
0.7778 Intermediate Similarity NPC24443
0.7761 Intermediate Similarity NPC309300
0.7761 Intermediate Similarity NPC225415
0.7746 Intermediate Similarity NPC469343
0.7746 Intermediate Similarity NPC471662
0.7727 Intermediate Similarity NPC475251
0.7681 Intermediate Similarity NPC477791
0.7647 Intermediate Similarity NPC238352
0.7647 Intermediate Similarity NPC477009
0.7639 Intermediate Similarity NPC476709
0.7612 Intermediate Similarity NPC474155
0.7612 Intermediate Similarity NPC473759
0.7606 Intermediate Similarity NPC92801
0.7606 Intermediate Similarity NPC470041
0.7571 Intermediate Similarity NPC471238
0.7571 Intermediate Similarity NPC167527
0.7538 Intermediate Similarity NPC10017
0.7534 Intermediate Similarity NPC306727
0.75 Intermediate Similarity NPC290367
0.75 Intermediate Similarity NPC41886
0.75 Intermediate Similarity NPC164022
0.75 Intermediate Similarity NPC62755
0.7467 Intermediate Similarity NPC130136
0.7465 Intermediate Similarity NPC74722
0.7465 Intermediate Similarity NPC304690
0.7465 Intermediate Similarity NPC471560
0.7463 Intermediate Similarity NPC63111
0.7432 Intermediate Similarity NPC60818
0.7432 Intermediate Similarity NPC23231
0.7429 Intermediate Similarity NPC136813
0.7429 Intermediate Similarity NPC259299
0.7429 Intermediate Similarity NPC73603
0.7424 Intermediate Similarity NPC122239
0.7397 Intermediate Similarity NPC329763
0.7397 Intermediate Similarity NPC68443
0.7397 Intermediate Similarity NPC474140
0.7391 Intermediate Similarity NPC300442
0.7391 Intermediate Similarity NPC19569
0.7391 Intermediate Similarity NPC308844
0.7368 Intermediate Similarity NPC475980
0.7361 Intermediate Similarity NPC471781
0.7361 Intermediate Similarity NPC34834
0.7333 Intermediate Similarity NPC126969
0.7333 Intermediate Similarity NPC253190
0.7324 Intermediate Similarity NPC305698
0.7324 Intermediate Similarity NPC208999
0.7324 Intermediate Similarity NPC96484
0.7313 Intermediate Similarity NPC66020
0.7297 Intermediate Similarity NPC471659
0.7286 Intermediate Similarity NPC272125
0.7286 Intermediate Similarity NPC267027
0.7273 Intermediate Similarity NPC475830
0.7273 Intermediate Similarity NPC325869
0.7273 Intermediate Similarity NPC226848
0.726 Intermediate Similarity NPC477792
0.726 Intermediate Similarity NPC471272
0.726 Intermediate Similarity NPC242001
0.726 Intermediate Similarity NPC167706
0.7237 Intermediate Similarity NPC476007
0.7237 Intermediate Similarity NPC471454
0.7237 Intermediate Similarity NPC476703
0.7237 Intermediate Similarity NPC471798
0.7222 Intermediate Similarity NPC239373
0.7222 Intermediate Similarity NPC217570
0.7222 Intermediate Similarity NPC474248
0.7222 Intermediate Similarity NPC329989
0.7222 Intermediate Similarity NPC90115
0.7206 Intermediate Similarity NPC321867
0.7206 Intermediate Similarity NPC68679
0.7206 Intermediate Similarity NPC207007
0.72 Intermediate Similarity NPC319090
0.72 Intermediate Similarity NPC474885
0.72 Intermediate Similarity NPC291503
0.72 Intermediate Similarity NPC32832
0.72 Intermediate Similarity NPC328104
0.7188 Intermediate Similarity NPC286752
0.7183 Intermediate Similarity NPC82337
0.7183 Intermediate Similarity NPC69649
0.7183 Intermediate Similarity NPC68703
0.7183 Intermediate Similarity NPC114651
0.7183 Intermediate Similarity NPC253303
0.7183 Intermediate Similarity NPC472253
0.7183 Intermediate Similarity NPC269077
0.7183 Intermediate Similarity NPC472255
0.7183 Intermediate Similarity NPC476650
0.7179 Intermediate Similarity NPC96362
0.7179 Intermediate Similarity NPC287749
0.7164 Intermediate Similarity NPC475931
0.7164 Intermediate Similarity NPC5698
0.7162 Intermediate Similarity NPC471799
0.7162 Intermediate Similarity NPC310608
0.7162 Intermediate Similarity NPC234527
0.7162 Intermediate Similarity NPC14352
0.7143 Intermediate Similarity NPC11555
0.7143 Intermediate Similarity NPC60837
0.7143 Intermediate Similarity NPC477089
0.7143 Intermediate Similarity NPC205618
0.7143 Intermediate Similarity NPC87604
0.7143 Intermediate Similarity NPC469326
0.7143 Intermediate Similarity NPC172613
0.7143 Intermediate Similarity NPC282619
0.7143 Intermediate Similarity NPC261782
0.7143 Intermediate Similarity NPC2728
0.7143 Intermediate Similarity NPC208198
0.7125 Intermediate Similarity NPC231601
0.7125 Intermediate Similarity NPC113978
0.7123 Intermediate Similarity NPC254845
0.7123 Intermediate Similarity NPC145498
0.7105 Intermediate Similarity NPC1973
0.7105 Intermediate Similarity NPC477925
0.7105 Intermediate Similarity NPC167873
0.7105 Intermediate Similarity NPC471658
0.7105 Intermediate Similarity NPC274079
0.7101 Intermediate Similarity NPC279200
0.7101 Intermediate Similarity NPC83200
0.7101 Intermediate Similarity NPC50435
0.7089 Intermediate Similarity NPC471661
0.7089 Intermediate Similarity NPC476646
0.7083 Intermediate Similarity NPC245795
0.7067 Intermediate Similarity NPC329090
0.7067 Intermediate Similarity NPC91858
0.7067 Intermediate Similarity NPC243342
0.7067 Intermediate Similarity NPC477138
0.7067 Intermediate Similarity NPC471797
0.7067 Intermediate Similarity NPC27395
0.7059 Intermediate Similarity NPC323153
0.7059 Intermediate Similarity NPC240506
0.7059 Intermediate Similarity NPC135648
0.7051 Intermediate Similarity NPC472463
0.7051 Intermediate Similarity NPC86971
0.7042 Intermediate Similarity NPC162309
0.7042 Intermediate Similarity NPC202017
0.7042 Intermediate Similarity NPC326310
0.7042 Intermediate Similarity NPC149680
0.7027 Intermediate Similarity NPC23954
0.7027 Intermediate Similarity NPC471271
0.7027 Intermediate Similarity NPC471268
0.7013 Intermediate Similarity NPC34019
0.7013 Intermediate Similarity NPC31037
0.7 Intermediate Similarity NPC287744
0.7 Intermediate Similarity NPC470614
0.7 Intermediate Similarity NPC210560
0.7 Intermediate Similarity NPC101128
0.7 Intermediate Similarity NPC1272
0.7 Intermediate Similarity NPC24824
0.7 Intermediate Similarity NPC219940
0.7 Intermediate Similarity NPC140233
0.7 Intermediate Similarity NPC96793
0.7 Intermediate Similarity NPC144650
0.7 Intermediate Similarity NPC87439
0.7 Intermediate Similarity NPC107540
0.7 Intermediate Similarity NPC323424
0.7 Intermediate Similarity NPC165651
0.7 Intermediate Similarity NPC110241
0.6986 Remote Similarity NPC473893
0.6986 Remote Similarity NPC144647
0.6986 Remote Similarity NPC16964
0.6974 Remote Similarity NPC133580
0.6974 Remote Similarity NPC66566
0.6974 Remote Similarity NPC477923
0.6974 Remote Similarity NPC113639
0.6974 Remote Similarity NPC114236
0.6974 Remote Similarity NPC313185
0.6974 Remote Similarity NPC93213
0.697 Remote Similarity NPC48891
0.6962 Remote Similarity NPC324772
0.6962 Remote Similarity NPC26117
0.6962 Remote Similarity NPC471266
0.6962 Remote Similarity NPC95124
0.6957 Remote Similarity NPC274704
0.6944 Remote Similarity NPC96962
0.6944 Remote Similarity NPC161612
0.6944 Remote Similarity NPC139207
0.6944 Remote Similarity NPC197805
0.6944 Remote Similarity NPC171225
0.6944 Remote Similarity NPC185874
0.6944 Remote Similarity NPC33583
0.6933 Remote Similarity NPC275098
0.6933 Remote Similarity NPC130665
0.6933 Remote Similarity NPC95165
0.6933 Remote Similarity NPC182717
0.6923 Remote Similarity NPC138621
0.6923 Remote Similarity NPC476314
0.6923 Remote Similarity NPC167037
0.6923 Remote Similarity NPC244385
0.6923 Remote Similarity NPC6978
0.6923 Remote Similarity NPC302041

  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 NPC61503 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.7206 Intermediate Similarity NPD368 Approved
0.7067 Intermediate Similarity NPD6924 Approved
0.7067 Intermediate Similarity NPD6926 Approved
0.7051 Intermediate Similarity NPD6929 Approved
0.6962 Remote Similarity NPD6931 Approved
0.6962 Remote Similarity NPD6930 Phase 2
0.6883 Remote Similarity NPD6933 Approved
0.6883 Remote Similarity NPD3701 Clinical (unspecified phase)
0.6875 Remote Similarity NPD6902 Approved
0.6829 Remote Similarity NPD7338 Clinical (unspecified phase)
0.6818 Remote Similarity NPD342 Phase 1
0.6795 Remote Similarity NPD6932 Approved
0.6795 Remote Similarity NPD5776 Phase 2
0.6795 Remote Similarity NPD6925 Approved
0.6757 Remote Similarity NPD6922 Approved
0.6757 Remote Similarity NPD6923 Approved
0.6753 Remote Similarity NPD7339 Approved
0.6753 Remote Similarity NPD6942 Approved
0.675 Remote Similarity NPD7525 Registered
0.675 Remote Similarity NPD7509 Discontinued
0.6709 Remote Similarity NPD7145 Approved
0.6707 Remote Similarity NPD6695 Phase 3
0.6667 Remote Similarity NPD7144 Approved
0.6667 Remote Similarity NPD7143 Approved
0.6625 Remote Similarity NPD7645 Phase 2
0.6625 Remote Similarity NPD6683 Phase 2
0.6579 Remote Similarity NPD7150 Approved
0.6579 Remote Similarity NPD7151 Approved
0.6579 Remote Similarity NPD7152 Approved
0.6548 Remote Similarity NPD6893 Approved
0.6543 Remote Similarity NPD7332 Phase 2
0.6543 Remote Similarity NPD7514 Phase 3
0.6538 Remote Similarity NPD8264 Approved
0.6463 Remote Similarity NPD6898 Phase 1
0.6395 Remote Similarity NPD4751 Clinical (unspecified phase)
0.6395 Remote Similarity NPD7750 Discontinued
0.6395 Remote Similarity NPD7524 Approved
0.6386 Remote Similarity NPD3667 Approved
0.6296 Remote Similarity NPD7322 Clinical (unspecified phase)
0.6282 Remote Similarity NPD4732 Discontinued
0.6235 Remote Similarity NPD3665 Phase 1
0.6235 Remote Similarity NPD3666 Approved
0.6235 Remote Similarity NPD3133 Approved
0.6235 Remote Similarity NPD4786 Approved
0.6154 Remote Similarity NPD4243 Approved
0.6111 Remote Similarity NPD7087 Discontinued
0.6098 Remote Similarity NPD5784 Clinical (unspecified phase)
0.6092 Remote Similarity NPD5279 Phase 3
0.6092 Remote Similarity NPD3618 Phase 1
0.6 Remote Similarity NPD4784 Approved
0.6 Remote Similarity NPD4219 Approved
0.6 Remote Similarity NPD4785 Approved
0.6 Remote Similarity NPD7838 Discovery
0.5978 Remote Similarity NPD5282 Discontinued
0.5952 Remote Similarity NPD4822 Approved
0.5952 Remote Similarity NPD5368 Approved
0.5952 Remote Similarity NPD4748 Discontinued
0.5952 Remote Similarity NPD4820 Approved
0.5952 Remote Similarity NPD4821 Approved
0.5952 Remote Similarity NPD4819 Approved
0.5926 Remote Similarity NPD4190 Phase 3
0.5926 Remote Similarity NPD5275 Approved
0.5904 Remote Similarity NPD4271 Approved
0.5904 Remote Similarity NPD4268 Approved
0.5889 Remote Similarity NPD5328 Approved
0.587 Remote Similarity NPD4202 Approved
0.5846 Remote Similarity NPD385 Approved
0.5846 Remote Similarity NPD384 Approved
0.5833 Remote Similarity NPD4195 Approved
0.5824 Remote Similarity NPD46 Approved
0.5824 Remote Similarity NPD7136 Phase 2
0.5824 Remote Similarity NPD6698 Approved
0.5824 Remote Similarity NPD3168 Discontinued
0.5814 Remote Similarity NPD6435 Approved
0.5795 Remote Similarity NPD1696 Phase 3
0.5795 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5789 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5765 Remote Similarity NPD4695 Discontinued
0.5765 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5761 Remote Similarity NPD6411 Approved
0.5761 Remote Similarity NPD6079 Approved
0.5761 Remote Similarity NPD7515 Phase 2
0.5761 Remote Similarity NPD7637 Suspended
0.5747 Remote Similarity NPD5362 Discontinued
0.5747 Remote Similarity NPD5331 Approved
0.5747 Remote Similarity NPD5332 Approved
0.5745 Remote Similarity NPD1698 Clinical (unspecified phase)
0.573 Remote Similarity NPD4249 Approved
0.5729 Remote Similarity NPD7638 Approved
0.5714 Remote Similarity NPD7331 Phase 2
0.5714 Remote Similarity NPD4753 Phase 2
0.5699 Remote Similarity NPD6399 Phase 3
0.5699 Remote Similarity NPD5779 Approved
0.5699 Remote Similarity NPD5778 Approved
0.5698 Remote Similarity NPD4790 Discontinued
0.5698 Remote Similarity NPD5369 Approved
0.5696 Remote Similarity NPD15 Approved
0.5696 Remote Similarity NPD1082 Approved
0.5696 Remote Similarity NPD791 Approved
0.5692 Remote Similarity NPD4265 Approved
0.5692 Remote Similarity NPD388 Approved
0.5692 Remote Similarity NPD386 Approved
0.5682 Remote Similarity NPD3668 Phase 3
0.567 Remote Similarity NPD7640 Approved
0.567 Remote Similarity NPD7639 Approved
0.5667 Remote Similarity NPD4250 Approved
0.5667 Remote Similarity NPD4251 Approved
0.5663 Remote Similarity NPD1346 Approved
0.5632 Remote Similarity NPD4221 Approved
0.5632 Remote Similarity NPD4269 Approved
0.5632 Remote Similarity NPD4223 Phase 3
0.5632 Remote Similarity NPD4270 Approved
0.5631 Remote Similarity NPD6371 Approved
0.5625 Remote Similarity NPD4755 Approved
0.5618 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5612 Remote Similarity NPD5344 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