Structure

Physi-Chem Properties

Molecular Weight:  222.2
Volume:  257.037
LogP:  5.621
LogD:  3.967
LogS:  -4.261
# Rotatable Bonds:  0
TPSA:  9.23
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.554
Synthetic Accessibility Score:  3.803
Fsp3:  0.867
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.425
MDCK Permeability:  1.6051033526309766e-05
Pgp-inhibitor:  0.953
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.731
30% Bioavailability (F30%):  0.009

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.115
Plasma Protein Binding (PPB):  94.43912506103516%
Volume Distribution (VD):  1.789
Pgp-substrate:  4.57856559753418%

ADMET: Metabolism

CYP1A2-inhibitor:  0.203
CYP1A2-substrate:  0.314
CYP2C19-inhibitor:  0.287
CYP2C19-substrate:  0.873
CYP2C9-inhibitor:  0.316
CYP2C9-substrate:  0.415
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.477
CYP3A4-inhibitor:  0.161
CYP3A4-substrate:  0.242

ADMET: Excretion

Clearance (CL):  13.019
Half-life (T1/2):  0.113

ADMET: Toxicity

hERG Blockers:  0.035
Human Hepatotoxicity (H-HT):  0.608
Drug-inuced Liver Injury (DILI):  0.044
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.076
Maximum Recommended Daily Dose:  0.316
Skin Sensitization:  0.822
Carcinogencity:  0.885
Eye Corrosion:  0.747
Eye Irritation:  0.834
Respiratory Toxicity:  0.858

Download Data

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

  Natural Product: NPC474477

Natural Product ID:  NPC474477
Common Name*:   Arenaran A
IUPAC Name:   (3Z,6aS,10aS)-4,7,7,10a-tetramethyl-5,6,6a,8,9,10-hexahydro-2H-1-benzoxocine
Synonyms:  
Standard InCHIKey:  HOKZKIGIBSWAKP-QFGWSVGLSA-N
Standard InCHI:  InChI=1S/C15H26O/c1-12-6-7-13-14(2,3)9-5-10-15(13,4)16-11-8-12/h8,13H,5-7,9-11H2,1-4H3/b12-8-/t13-,15-/m0/s1
SMILES:  CC1=CCO[C@@]2([C@@H](CC1)C(C)(C)CCC2)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL469705
PubChem CID:   10376280
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001796] Oxocins

*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
NPO25382 Dysidea arenaria Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[7760077]
NPO25382 Dysidea arenaria Species Dysideidae 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
NPT81 Cell Line A549 Homo sapiens IC50 = 9.51 ug.mL-1 PMID[515924]
NPT139 Cell Line HT-29 Homo sapiens IC50 = 9.11 ug.mL-1 PMID[515924]
NPT5532 Cell Line HCT-29 IC50 = 5.28 ug.mL-1 PMID[515924]
NPT168 Cell Line P388 Mus musculus IC50 = 3.17 ug.mL-1 PMID[515924]

☑ 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 NPC474477 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
0.8732 High Similarity NPC470751
0.8636 High Similarity NPC327815
0.8219 Intermediate Similarity NPC470750
0.8116 Intermediate Similarity NPC476945
0.7692 Intermediate Similarity NPC155521
0.7647 Intermediate Similarity NPC81615
0.7632 Intermediate Similarity NPC184737
0.7606 Intermediate Similarity NPC139785
0.7568 Intermediate Similarity NPC201048
0.7568 Intermediate Similarity NPC476366
0.7536 Intermediate Similarity NPC225415
0.7534 Intermediate Similarity NPC471272
0.7534 Intermediate Similarity NPC477792
0.7532 Intermediate Similarity NPC233295
0.7467 Intermediate Similarity NPC32832
0.7436 Intermediate Similarity NPC474592
0.7436 Intermediate Similarity NPC233332
0.7436 Intermediate Similarity NPC469802
0.7432 Intermediate Similarity NPC259049
0.7368 Intermediate Similarity NPC470749
0.7361 Intermediate Similarity NPC96484
0.7361 Intermediate Similarity NPC471238
0.7342 Intermediate Similarity NPC25554
0.7324 Intermediate Similarity NPC42630
0.7308 Intermediate Similarity NPC242767
0.7297 Intermediate Similarity NPC167706
0.7297 Intermediate Similarity NPC471271
0.7297 Intermediate Similarity NPC23954
0.7297 Intermediate Similarity NPC164022
0.7297 Intermediate Similarity NPC471268
0.7286 Intermediate Similarity NPC329698
0.7284 Intermediate Similarity NPC96055
0.7284 Intermediate Similarity NPC46320
0.7284 Intermediate Similarity NPC470077
0.7273 Intermediate Similarity NPC470711
0.7273 Intermediate Similarity NPC189206
0.7273 Intermediate Similarity NPC470758
0.726 Intermediate Similarity NPC474248
0.725 Intermediate Similarity NPC304285
0.725 Intermediate Similarity NPC470049
0.725 Intermediate Similarity NPC259858
0.7246 Intermediate Similarity NPC194208
0.7246 Intermediate Similarity NPC282694
0.7246 Intermediate Similarity NPC79576
0.7237 Intermediate Similarity NPC133580
0.7229 Intermediate Similarity NPC166857
0.7229 Intermediate Similarity NPC476948
0.7222 Intermediate Similarity NPC68703
0.7222 Intermediate Similarity NPC69649
0.7222 Intermediate Similarity NPC171225
0.7215 Intermediate Similarity NPC206062
0.72 Intermediate Similarity NPC265485
0.72 Intermediate Similarity NPC220939
0.7195 Intermediate Similarity NPC474013
0.7195 Intermediate Similarity NPC476678
0.7183 Intermediate Similarity NPC258595
0.7162 Intermediate Similarity NPC34834
0.7162 Intermediate Similarity NPC92801
0.716 Intermediate Similarity NPC23748
0.716 Intermediate Similarity NPC470558
0.716 Intermediate Similarity NPC476927
0.716 Intermediate Similarity NPC49208
0.7143 Intermediate Similarity NPC93411
0.7143 Intermediate Similarity NPC283247
0.7143 Intermediate Similarity NPC174956
0.7143 Intermediate Similarity NPC265588
0.7125 Intermediate Similarity NPC170303
0.7123 Intermediate Similarity NPC94192
0.7108 Intermediate Similarity NPC255143
0.7108 Intermediate Similarity NPC471219
0.7108 Intermediate Similarity NPC323209
0.7108 Intermediate Similarity NPC131813
0.7105 Intermediate Similarity NPC309178
0.7105 Intermediate Similarity NPC306727
0.7105 Intermediate Similarity NPC78527
0.7101 Intermediate Similarity NPC135648
0.7089 Intermediate Similarity NPC17550
0.7083 Intermediate Similarity NPC279434
0.7083 Intermediate Similarity NPC116013
0.7083 Intermediate Similarity NPC202017
0.7073 Intermediate Similarity NPC83702
0.7073 Intermediate Similarity NPC306951
0.7059 Intermediate Similarity NPC189290
0.7059 Intermediate Similarity NPC474769
0.7051 Intermediate Similarity NPC474826
0.7051 Intermediate Similarity NPC91594
0.7051 Intermediate Similarity NPC477427
0.7051 Intermediate Similarity NPC219809
0.7051 Intermediate Similarity NPC283619
0.7051 Intermediate Similarity NPC477425
0.7051 Intermediate Similarity NPC477426
0.7042 Intermediate Similarity NPC101128
0.7042 Intermediate Similarity NPC96793
0.7042 Intermediate Similarity NPC323424
0.7042 Intermediate Similarity NPC107540
0.7042 Intermediate Similarity NPC287744
0.7042 Intermediate Similarity NPC140233
0.7037 Intermediate Similarity NPC122945
0.7037 Intermediate Similarity NPC109938
0.7037 Intermediate Similarity NPC471408
0.7037 Intermediate Similarity NPC471218
0.7037 Intermediate Similarity NPC256112
0.7027 Intermediate Similarity NPC473893
0.7027 Intermediate Similarity NPC476431
0.7015 Intermediate Similarity NPC210316
0.7015 Intermediate Similarity NPC39068
0.7 Intermediate Similarity NPC195424
0.7 Intermediate Similarity NPC268827
0.6988 Remote Similarity NPC472442
0.6988 Remote Similarity NPC477578
0.6988 Remote Similarity NPC274448
0.6988 Remote Similarity NPC35933
0.6988 Remote Similarity NPC157257
0.6986 Remote Similarity NPC114651
0.6974 Remote Similarity NPC182717
0.6962 Remote Similarity NPC476314
0.6957 Remote Similarity NPC83838
0.6957 Remote Similarity NPC143810
0.6951 Remote Similarity NPC222358
0.6951 Remote Similarity NPC311070
0.6951 Remote Similarity NPC472377
0.6944 Remote Similarity NPC474768
0.6941 Remote Similarity NPC106332
0.6941 Remote Similarity NPC471952
0.6941 Remote Similarity NPC473879
0.6941 Remote Similarity NPC477128
0.6933 Remote Similarity NPC145498
0.6923 Remote Similarity NPC167873
0.6923 Remote Similarity NPC476317
0.6923 Remote Similarity NPC1973
0.6923 Remote Similarity NPC253190
0.6914 Remote Similarity NPC70927
0.6914 Remote Similarity NPC249423
0.6914 Remote Similarity NPC474759
0.6914 Remote Similarity NPC82986
0.6914 Remote Similarity NPC474683
0.6914 Remote Similarity NPC7505
0.6914 Remote Similarity NPC474752
0.6914 Remote Similarity NPC14203
0.6914 Remote Similarity NPC229584
0.6914 Remote Similarity NPC474731
0.6912 Remote Similarity NPC11130
0.6905 Remote Similarity NPC329692
0.6905 Remote Similarity NPC102996
0.6905 Remote Similarity NPC286153
0.6897 Remote Similarity NPC49420
0.6892 Remote Similarity NPC208999
0.6883 Remote Similarity NPC100334
0.6883 Remote Similarity NPC91858
0.6883 Remote Similarity NPC243342
0.6883 Remote Similarity NPC71152
0.6883 Remote Similarity NPC477138
0.6875 Remote Similarity NPC283789
0.6867 Remote Similarity NPC474047
0.6867 Remote Similarity NPC32223
0.6867 Remote Similarity NPC15534
0.6866 Remote Similarity NPC223604
0.686 Remote Similarity NPC470819
0.686 Remote Similarity NPC246028
0.686 Remote Similarity NPC82876
0.6857 Remote Similarity NPC240506
0.6857 Remote Similarity NPC127824
0.6857 Remote Similarity NPC66020
0.6849 Remote Similarity NPC149680
0.6849 Remote Similarity NPC476406
0.6842 Remote Similarity NPC242001
0.6842 Remote Similarity NPC110799
0.6842 Remote Similarity NPC242992
0.6835 Remote Similarity NPC149550
0.6835 Remote Similarity NPC471454
0.6835 Remote Similarity NPC132542
0.6835 Remote Similarity NPC85105
0.6835 Remote Similarity NPC169994
0.6835 Remote Similarity NPC474230
0.6835 Remote Similarity NPC54996
0.6829 Remote Similarity NPC2524
0.6829 Remote Similarity NPC218616
0.6829 Remote Similarity NPC296701
0.6829 Remote Similarity NPC87489
0.6829 Remote Similarity NPC200513
0.6824 Remote Similarity NPC149224
0.6824 Remote Similarity NPC474832
0.6824 Remote Similarity NPC131329
0.6824 Remote Similarity NPC231599
0.6824 Remote Similarity NPC102640
0.6818 Remote Similarity NPC7349
0.6818 Remote Similarity NPC165755
0.6806 Remote Similarity NPC68656
0.6806 Remote Similarity NPC219940
0.6806 Remote Similarity NPC144650
0.6806 Remote Similarity NPC290367
0.68 Remote Similarity NPC9942
0.68 Remote Similarity NPC471560
0.6795 Remote Similarity NPC291503
0.6795 Remote Similarity NPC313185
0.6795 Remote Similarity NPC66566
0.6795 Remote Similarity NPC477923
0.679 Remote Similarity NPC148685
0.679 Remote Similarity NPC471266
0.679 Remote Similarity NPC157895

  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 NPC474477 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
0.6829 Remote Similarity NPD4752 Clinical (unspecified phase)
0.6667 Remote Similarity NPD7645 Phase 2
0.6667 Remote Similarity NPD6051 Approved
0.6588 Remote Similarity NPD1694 Approved
0.6585 Remote Similarity NPD7525 Registered
0.6528 Remote Similarity NPD368 Approved
0.6486 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6456 Remote Similarity NPD6926 Approved
0.6456 Remote Similarity NPD6924 Approved
0.641 Remote Similarity NPD4243 Approved
0.6377 Remote Similarity NPD342 Phase 1
0.6375 Remote Similarity NPD7339 Approved
0.6375 Remote Similarity NPD8264 Approved
0.6375 Remote Similarity NPD8039 Approved
0.6375 Remote Similarity NPD6942 Approved
0.6353 Remote Similarity NPD6695 Phase 3
0.6351 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6296 Remote Similarity NPD6933 Approved
0.6296 Remote Similarity NPD3701 Clinical (unspecified phase)
0.6279 Remote Similarity NPD7338 Clinical (unspecified phase)
0.6277 Remote Similarity NPD7638 Approved
0.6277 Remote Similarity NPD4225 Approved
0.625 Remote Similarity NPD4785 Approved
0.625 Remote Similarity NPD4784 Approved
0.6211 Remote Similarity NPD7639 Approved
0.6211 Remote Similarity NPD7640 Approved
0.619 Remote Similarity NPD7509 Discontinued
0.619 Remote Similarity NPD6930 Phase 2
0.619 Remote Similarity NPD6931 Approved
0.6173 Remote Similarity NPD5275 Approved
0.6173 Remote Similarity NPD4190 Phase 3
0.6164 Remote Similarity NPD1145 Discontinued
0.6154 Remote Similarity NPD6923 Approved
0.6154 Remote Similarity NPD6922 Approved
0.6145 Remote Similarity NPD7322 Clinical (unspecified phase)
0.6076 Remote Similarity NPD7144 Approved
0.6076 Remote Similarity NPD7143 Approved
0.6071 Remote Similarity NPD6929 Approved
0.6067 Remote Similarity NPD7524 Approved
0.6067 Remote Similarity NPD3573 Approved
0.6067 Remote Similarity NPD7750 Discontinued
0.6067 Remote Similarity NPD4751 Clinical (unspecified phase)
0.6056 Remote Similarity NPD4219 Approved
0.6 Remote Similarity NPD7150 Approved
0.6 Remote Similarity NPD7151 Approved
0.6 Remote Similarity NPD7152 Approved
0.6 Remote Similarity NPD7332 Phase 2
0.6 Remote Similarity NPD7514 Phase 3
0.5978 Remote Similarity NPD5693 Phase 1
0.597 Remote Similarity NPD9410 Clinical (unspecified phase)
0.5955 Remote Similarity NPD6409 Approved
0.5955 Remote Similarity NPD7334 Approved
0.5955 Remote Similarity NPD5330 Approved
0.5955 Remote Similarity NPD6684 Approved
0.5955 Remote Similarity NPD7146 Approved
0.5955 Remote Similarity NPD3618 Phase 1
0.5955 Remote Similarity NPD7521 Approved
0.5882 Remote Similarity NPD4195 Approved
0.5876 Remote Similarity NPD6648 Approved
0.5862 Remote Similarity NPD3667 Approved
0.5851 Remote Similarity NPD7901 Clinical (unspecified phase)
0.5851 Remote Similarity NPD7900 Approved
0.5851 Remote Similarity NPD7748 Approved
0.5843 Remote Similarity NPD6893 Approved
0.5833 Remote Similarity NPD6932 Approved
0.5833 Remote Similarity NPD5776 Phase 2
0.5833 Remote Similarity NPD6925 Approved
0.5824 Remote Similarity NPD5737 Approved
0.5824 Remote Similarity NPD7513 Clinical (unspecified phase)
0.5824 Remote Similarity NPD6903 Approved
0.5824 Remote Similarity NPD6672 Approved
0.5816 Remote Similarity NPD4159 Approved
0.5816 Remote Similarity NPD5344 Discontinued
0.5814 Remote Similarity NPD4748 Discontinued
0.5806 Remote Similarity NPD7087 Discontinued
0.5789 Remote Similarity NPD6356 Clinical (unspecified phase)
0.5781 Remote Similarity NPD1799 Clinical (unspecified phase)
0.5778 Remote Similarity NPD6098 Approved
0.5778 Remote Similarity NPD4519 Discontinued
0.5778 Remote Similarity NPD4623 Approved
0.5765 Remote Similarity NPD7145 Approved
0.5761 Remote Similarity NPD5328 Approved
0.5747 Remote Similarity NPD6898 Phase 1
0.5747 Remote Similarity NPD6902 Approved
0.5745 Remote Similarity NPD4202 Approved
0.573 Remote Similarity NPD3133 Approved
0.573 Remote Similarity NPD4786 Approved
0.573 Remote Similarity NPD3665 Phase 1
0.573 Remote Similarity NPD3668 Phase 3
0.573 Remote Similarity NPD3666 Approved
0.5699 Remote Similarity NPD3168 Discontinued
0.5698 Remote Similarity NPD6683 Phase 2
0.5684 Remote Similarity NPD6001 Approved
0.5682 Remote Similarity NPD4223 Phase 3
0.5682 Remote Similarity NPD5209 Approved
0.5682 Remote Similarity NPD4221 Approved
0.567 Remote Similarity NPD7902 Approved
0.5667 Remote Similarity NPD1696 Phase 3
0.5652 Remote Similarity NPD5208 Approved
0.5638 Remote Similarity NPD7515 Phase 2
0.5638 Remote Similarity NPD6079 Approved
0.5632 Remote Similarity NPD4695 Discontinued
0.5625 Remote Similarity NPD5695 Phase 3
0.5604 Remote Similarity NPD5279 Phase 3
0.5604 Remote Similarity NPD3574 Clinical (unspecified phase)
0.56 Remote Similarity NPD7632 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