Structure

Physi-Chem Properties

Molecular Weight:  386.18
Volume:  365.671
LogP:  5.026
LogD:  4.387
LogS:  -5.427
# Rotatable Bonds:  1
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.637
Synthetic Accessibility Score:  4.686
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.566
MDCK Permeability:  1.6350912119378336e-05
Pgp-inhibitor:  0.99
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.406
30% Bioavailability (F30%):  0.806

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.276
Plasma Protein Binding (PPB):  95.42105102539062%
Volume Distribution (VD):  1.191
Pgp-substrate:  3.679398536682129%

ADMET: Metabolism

CYP1A2-inhibitor:  0.195
CYP1A2-substrate:  0.441
CYP2C19-inhibitor:  0.146
CYP2C19-substrate:  0.912
CYP2C9-inhibitor:  0.497
CYP2C9-substrate:  0.146
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.191
CYP3A4-inhibitor:  0.439
CYP3A4-substrate:  0.472

ADMET: Excretion

Clearance (CL):  9.219
Half-life (T1/2):  0.129

ADMET: Toxicity

hERG Blockers:  0.501
Human Hepatotoxicity (H-HT):  0.232
Drug-inuced Liver Injury (DILI):  0.703
AMES Toxicity:  0.032
Rat Oral Acute Toxicity:  0.641
Maximum Recommended Daily Dose:  0.019
Skin Sensitization:  0.911
Carcinogencity:  0.378
Eye Corrosion:  0.96
Eye Irritation:  0.298
Respiratory Toxicity:  0.974

Download Data

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

  Natural Product: NPC476422

Natural Product ID:  NPC476422
Common Name*:   Neodolastane
IUPAC Name:   (3S,3aS,5aS,6S,9R,9aR,10R,10aS)-6-bromo-3a,5a,9-trimethyl-3-propan-2-yl-2,3,4,5,6,7,8,9a,10,10a-decahydro-1H-benzo[f]azulene-9,10-diol
Synonyms:   Neodolastane
Standard InCHIKey:  DDQRJEVPJMWPLK-FQBPZLHKSA-N
Standard InCHI:  InChI=1S/C20H35BrO2/c1-12(2)13-6-7-14-16(22)17-19(4,11-10-18(13,14)3)15(21)8-9-20(17,5)23/h12-17,22-23H,6-11H2,1-5H3/t13-,14+,15-,16+,17-,18-,19+,20+/m0/s1
SMILES:  CC(C)C1CCC2C1(CCC3(C(CCC(C3C2O)(C)O)Br)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL599309
PubChem CID:   46232272
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001670] Tertiary 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
NPO29354 Sphaerococcus coronopifolius Species Sphaerococcaceae Eukaryota n.a. n.a. n.a. PMID[11520219]
NPO29354 Sphaerococcus coronopifolius Species Sphaerococcaceae Eukaryota n.a. n.a. n.a. PMID[18597527]
NPO29354 Sphaerococcus coronopifolius Species Sphaerococcaceae Eukaryota n.a. n.a. n.a. PMID[20045651]
NPO29354 Sphaerococcus coronopifolius Species Sphaerococcaceae 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 = 97000.0 nM PMID[453900]
NPT170 Cell Line SK-MEL-28 Homo sapiens IC50 = 96000.0 nM PMID[453900]
NPT306 Cell Line PC-3 Homo sapiens IC50 = 74000.0 nM PMID[453900]
NPT114 Cell Line LoVo Homo sapiens IC50 = 64000.0 nM PMID[453900]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 85000.0 nM PMID[453900]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 60000.0 nM PMID[453900]

☑ 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 NPC476422 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
0.8421 Intermediate Similarity NPC329871
0.8 Intermediate Similarity NPC237510
0.8 Intermediate Similarity NPC475793
0.7895 Intermediate Similarity NPC476424
0.7561 Intermediate Similarity NPC163616
0.7465 Intermediate Similarity NPC185547
0.7465 Intermediate Similarity NPC95804
0.7326 Intermediate Similarity NPC475817
0.7237 Intermediate Similarity NPC107919
0.7215 Intermediate Similarity NPC139765
0.7215 Intermediate Similarity NPC131584
0.72 Intermediate Similarity NPC473230
0.72 Intermediate Similarity NPC475884
0.72 Intermediate Similarity NPC48079
0.7162 Intermediate Similarity NPC472946
0.7123 Intermediate Similarity NPC114891
0.7105 Intermediate Similarity NPC472741
0.7105 Intermediate Similarity NPC474756
0.7067 Intermediate Similarity NPC142712
0.7013 Intermediate Similarity NPC470830
0.7013 Intermediate Similarity NPC129829
0.7013 Intermediate Similarity NPC66407
0.7013 Intermediate Similarity NPC254037
0.7013 Intermediate Similarity NPC241085
0.7013 Intermediate Similarity NPC299948
0.6986 Remote Similarity NPC218585
0.6986 Remote Similarity NPC71460
0.6986 Remote Similarity NPC148174
0.6977 Remote Similarity NPC313115
0.6974 Remote Similarity NPC63190
0.6962 Remote Similarity NPC476609
0.6933 Remote Similarity NPC473276
0.6933 Remote Similarity NPC80463
0.6933 Remote Similarity NPC474380
0.6933 Remote Similarity NPC41577
0.6923 Remote Similarity NPC192192
0.6923 Remote Similarity NPC231945
0.6923 Remote Similarity NPC282454
0.6901 Remote Similarity NPC135438
0.6901 Remote Similarity NPC291147
0.6897 Remote Similarity NPC475276
0.6875 Remote Similarity NPC304499
0.6875 Remote Similarity NPC10476
0.6875 Remote Similarity NPC192501
0.6875 Remote Similarity NPC228994
0.6857 Remote Similarity NPC471269
0.6842 Remote Similarity NPC44122
0.6835 Remote Similarity NPC1340
0.6835 Remote Similarity NPC157422
0.6835 Remote Similarity NPC473279
0.6835 Remote Similarity NPC252182
0.6835 Remote Similarity NPC195530
0.6835 Remote Similarity NPC127094
0.6835 Remote Similarity NPC187471
0.6835 Remote Similarity NPC131506
0.6835 Remote Similarity NPC109457
0.6835 Remote Similarity NPC470071
0.6835 Remote Similarity NPC100586
0.6835 Remote Similarity NPC157777
0.6818 Remote Similarity NPC174273
0.6806 Remote Similarity NPC87296
0.6806 Remote Similarity NPC476735
0.6806 Remote Similarity NPC215671
0.6806 Remote Similarity NPC475515
0.68 Remote Similarity NPC69149
0.68 Remote Similarity NPC118937
0.68 Remote Similarity NPC281540
0.68 Remote Similarity NPC167995
0.68 Remote Similarity NPC159654
0.68 Remote Similarity NPC219940
0.6795 Remote Similarity NPC477820
0.679 Remote Similarity NPC476605
0.679 Remote Similarity NPC158208
0.679 Remote Similarity NPC196136
0.679 Remote Similarity NPC243027
0.679 Remote Similarity NPC317242
0.6786 Remote Similarity NPC117137
0.6786 Remote Similarity NPC66766
0.675 Remote Similarity NPC473238
0.675 Remote Similarity NPC153719
0.675 Remote Similarity NPC472341
0.6742 Remote Similarity NPC188896
0.6742 Remote Similarity NPC131453
0.6712 Remote Similarity NPC95958
0.6711 Remote Similarity NPC475943
0.6711 Remote Similarity NPC243469
0.6711 Remote Similarity NPC190827
0.6709 Remote Similarity NPC251201
0.6709 Remote Similarity NPC232925
0.6709 Remote Similarity NPC63588
0.6707 Remote Similarity NPC163597
0.6707 Remote Similarity NPC470145
0.6706 Remote Similarity NPC473257
0.6667 Remote Similarity NPC236099
0.6667 Remote Similarity NPC239453
0.6667 Remote Similarity NPC29976
0.6667 Remote Similarity NPC476610
0.6667 Remote Similarity NPC209686
0.6667 Remote Similarity NPC475458
0.6667 Remote Similarity NPC236588
0.6667 Remote Similarity NPC249078
0.6667 Remote Similarity NPC150713
0.6667 Remote Similarity NPC224552
0.6667 Remote Similarity NPC478130
0.6667 Remote Similarity NPC477508
0.6627 Remote Similarity NPC128951
0.6627 Remote Similarity NPC302578
0.6627 Remote Similarity NPC476233
0.6627 Remote Similarity NPC192046
0.6627 Remote Similarity NPC477227
0.6627 Remote Similarity NPC133596
0.6627 Remote Similarity NPC185915
0.6627 Remote Similarity NPC105208
0.6627 Remote Similarity NPC11907
0.6625 Remote Similarity NPC478103
0.6625 Remote Similarity NPC8004
0.6625 Remote Similarity NPC127283
0.6585 Remote Similarity NPC3403
0.6585 Remote Similarity NPC231680
0.6585 Remote Similarity NPC91387
0.6585 Remote Similarity NPC270306
0.6582 Remote Similarity NPC99264
0.6552 Remote Similarity NPC29342
0.6552 Remote Similarity NPC2572
0.6548 Remote Similarity NPC18857
0.6548 Remote Similarity NPC147993
0.6548 Remote Similarity NPC67657
0.6548 Remote Similarity NPC471769
0.6548 Remote Similarity NPC31828
0.6543 Remote Similarity NPC470610
0.6543 Remote Similarity NPC232112
0.6528 Remote Similarity NPC3025
0.6506 Remote Similarity NPC93662
0.6506 Remote Similarity NPC91573
0.6506 Remote Similarity NPC476606
0.6506 Remote Similarity NPC476607
0.6506 Remote Similarity NPC278091
0.6506 Remote Similarity NPC78067
0.6494 Remote Similarity NPC300442
0.6494 Remote Similarity NPC260116
0.6486 Remote Similarity NPC475968
0.6479 Remote Similarity NPC202146
0.6479 Remote Similarity NPC53209
0.6479 Remote Similarity NPC32222
0.6477 Remote Similarity NPC242016
0.6471 Remote Similarity NPC476603
0.6471 Remote Similarity NPC477282
0.6471 Remote Similarity NPC81074
0.6471 Remote Similarity NPC129501
0.6471 Remote Similarity NPC269333
0.6471 Remote Similarity NPC287452
0.6463 Remote Similarity NPC472945
0.6463 Remote Similarity NPC48795
0.6463 Remote Similarity NPC472944
0.6438 Remote Similarity NPC119425
0.6429 Remote Similarity NPC475031
0.6429 Remote Similarity NPC31037
0.6429 Remote Similarity NPC474574
0.6429 Remote Similarity NPC64081
0.6429 Remote Similarity NPC23884
0.642 Remote Similarity NPC58057
0.642 Remote Similarity NPC151018
0.642 Remote Similarity NPC156277
0.642 Remote Similarity NPC111234
0.642 Remote Similarity NPC320549
0.642 Remote Similarity NPC475077
0.6395 Remote Similarity NPC16449
0.6389 Remote Similarity NPC89069
0.6389 Remote Similarity NPC178223
0.6389 Remote Similarity NPC283655
0.6389 Remote Similarity NPC277917
0.6389 Remote Similarity NPC166894
0.6386 Remote Similarity NPC186851
0.6386 Remote Similarity NPC230704
0.6386 Remote Similarity NPC185536
0.6386 Remote Similarity NPC195155
0.6386 Remote Similarity NPC125767
0.6386 Remote Similarity NPC97534
0.6386 Remote Similarity NPC212879
0.6386 Remote Similarity NPC104387
0.6386 Remote Similarity NPC240235
0.6386 Remote Similarity NPC273366
0.6386 Remote Similarity NPC70982
0.6386 Remote Similarity NPC178383
0.6386 Remote Similarity NPC21220
0.6386 Remote Similarity NPC174964
0.6386 Remote Similarity NPC231256
0.6386 Remote Similarity NPC212733
0.6375 Remote Similarity NPC470833
0.6375 Remote Similarity NPC476604
0.6364 Remote Similarity NPC199937
0.6353 Remote Similarity NPC42853
0.6353 Remote Similarity NPC472501
0.6353 Remote Similarity NPC285761
0.6353 Remote Similarity NPC471045
0.6353 Remote Similarity NPC472342
0.6353 Remote Similarity NPC301707
0.6351 Remote Similarity NPC47663
0.6351 Remote Similarity NPC162685
0.6341 Remote Similarity NPC253805

  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 NPC476422 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
0.7237 Intermediate Similarity NPD4267 Clinical (unspecified phase)
0.6747 Remote Similarity NPD3671 Phase 1
0.6709 Remote Similarity NPD4787 Phase 1
0.642 Remote Similarity NPD4808 Clinical (unspecified phase)
0.642 Remote Similarity NPD4809 Clinical (unspecified phase)
0.631 Remote Similarity NPD6117 Approved
0.6282 Remote Similarity NPD3171 Clinical (unspecified phase)
0.6265 Remote Similarity NPD6113 Clinical (unspecified phase)
0.6235 Remote Similarity NPD6116 Phase 1
0.6207 Remote Similarity NPD7525 Registered
0.6176 Remote Similarity NPD385 Approved
0.6176 Remote Similarity NPD384 Approved
0.6173 Remote Similarity NPD3700 Clinical (unspecified phase)
0.6173 Remote Similarity NPD3699 Clinical (unspecified phase)
0.6163 Remote Similarity NPD6697 Approved
0.6163 Remote Similarity NPD6114 Approved
0.6163 Remote Similarity NPD6118 Approved
0.6163 Remote Similarity NPD6115 Approved
0.6098 Remote Similarity NPD4244 Approved
0.6098 Remote Similarity NPD4789 Approved
0.6098 Remote Similarity NPD4245 Approved
0.6071 Remote Similarity NPD6924 Approved
0.6071 Remote Similarity NPD6926 Approved
0.6049 Remote Similarity NPD5360 Phase 3
0.6049 Remote Similarity NPD6705 Phase 1
0.6049 Remote Similarity NPD5361 Clinical (unspecified phase)
0.6 Remote Similarity NPD3703 Phase 2
0.5976 Remote Similarity NPD3698 Phase 2
0.593 Remote Similarity NPD6933 Approved
0.5843 Remote Similarity NPD6930 Phase 2
0.5843 Remote Similarity NPD6928 Phase 2
0.5843 Remote Similarity NPD6931 Approved
0.5843 Remote Similarity NPD4748 Discontinued
0.5814 Remote Similarity NPD7339 Approved
0.5814 Remote Similarity NPD6942 Approved
0.573 Remote Similarity NPD6929 Approved
0.5699 Remote Similarity NPD7520 Clinical (unspecified phase)
0.5682 Remote Similarity NPD6932 Approved
0.5667 Remote Similarity NPD7509 Discontinued
0.5652 Remote Similarity NPD6695 Phase 3
0.5647 Remote Similarity NPD4758 Discontinued
0.5632 Remote Similarity NPD3702 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