Structure

Physi-Chem Properties

Molecular Weight:  236.18
Volume:  257.271
LogP:  3.535
LogD:  3.428
LogS:  -4.496
# Rotatable Bonds:  0
TPSA:  32.76
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.518
Synthetic Accessibility Score:  4.925
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:  -4.708
MDCK Permeability:  2.2217975129024126e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.009
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.062
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.328
Plasma Protein Binding (PPB):  57.5435791015625%
Volume Distribution (VD):  1.327
Pgp-substrate:  50.11309814453125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.049
CYP1A2-substrate:  0.172
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.846
CYP2C9-inhibitor:  0.083
CYP2C9-substrate:  0.265
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.717
CYP3A4-inhibitor:  0.034
CYP3A4-substrate:  0.292

ADMET: Excretion

Clearance (CL):  9.25
Half-life (T1/2):  0.313

ADMET: Toxicity

hERG Blockers:  0.372
Human Hepatotoxicity (H-HT):  0.966
Drug-inuced Liver Injury (DILI):  0.147
AMES Toxicity:  0.015
Rat Oral Acute Toxicity:  0.618
Maximum Recommended Daily Dose:  0.927
Skin Sensitization:  0.151
Carcinogencity:  0.039
Eye Corrosion:  0.141
Eye Irritation:  0.446
Respiratory Toxicity:  0.945

Download Data

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

  Natural Product: NPC161612

Natural Product ID:  NPC161612
Common Name*:   Suberosol B
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FWFSLBQGEMBSLF-FTQJZPFOSA-N
Standard InCHI:  InChI=1S/C15H24O2/c1-9-5-6-13-15(4,17-13)12(16)7-11-10(9)8-14(11,2)3/h10-13,16H,1,5-8H2,2-4H3/t10-,11-,12-,13-,15-/m1/s1
SMILES:  C=C1CC[C@H]2O[C@@]2([C@@H](C[C@@H]2[C@@H]1CC2(C)C)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL463055
PubChem CID:   10444136
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO11745 Subergorgia suberosa Species Subergorgiidae Eukaryota n.a. Taiwanese gorgonian coral n.a. PMID[12088433]
NPO11745 Subergorgia suberosa Species Subergorgiidae Eukaryota n.a. Taiwanese Gorgonian coral n.a. PMID[12141868]
NPO11745 Subergorgia suberosa Species Subergorgiidae Eukaryota n.a. n.a. n.a. PMID[16124781]
NPO11745 Subergorgia suberosa Species Subergorgiidae Eukaryota n.a. n.a. n.a. PMID[18290631]
NPO16051 Beilschmiedia erythrophloia Species Lauraceae Eukaryota Roots n.a. n.a. PMID[19072217]
NPO16051 Beilschmiedia erythrophloia Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11745 Subergorgia suberosa Species Subergorgiidae 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
NPT168 Cell Line P388 Mus musculus ED50 = 7.4 ug ml-1 PMID[529753]
NPT81 Cell Line A549 Homo sapiens ED50 > 50.0 ug ml-1 PMID[529753]
NPT139 Cell Line HT-29 Homo sapiens ED50 > 50.0 ug ml-1 PMID[529753]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC = 28.9 ug.mL-1 PMID[529754]

☑ 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 NPC161612 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
1.0 High Similarity NPC33583
0.8548 High Similarity NPC101285
0.8548 High Similarity NPC27853
0.8548 High Similarity NPC7491
0.8548 High Similarity NPC65786
0.8548 High Similarity NPC13789
0.8462 Intermediate Similarity NPC50435
0.8169 Intermediate Similarity NPC329763
0.8065 Intermediate Similarity NPC286752
0.7671 Intermediate Similarity NPC476709
0.7568 Intermediate Similarity NPC190859
0.7368 Intermediate Similarity NPC170148
0.7333 Intermediate Similarity NPC471525
0.7324 Intermediate Similarity NPC469328
0.7273 Intermediate Similarity NPC476703
0.72 Intermediate Similarity NPC143576
0.7179 Intermediate Similarity NPC52755
0.7179 Intermediate Similarity NPC475980
0.7179 Intermediate Similarity NPC477089
0.716 Intermediate Similarity NPC260852
0.7143 Intermediate Similarity NPC473759
0.7143 Intermediate Similarity NPC293223
0.7143 Intermediate Similarity NPC474155
0.7123 Intermediate Similarity NPC244790
0.7101 Intermediate Similarity NPC475412
0.7042 Intermediate Similarity NPC219940
0.7042 Intermediate Similarity NPC199937
0.7042 Intermediate Similarity NPC101128
0.7027 Intermediate Similarity NPC239373
0.7027 Intermediate Similarity NPC329989
0.7013 Intermediate Similarity NPC36479
0.7013 Intermediate Similarity NPC474419
0.7 Intermediate Similarity NPC475807
0.6944 Remote Similarity NPC471200
0.6944 Remote Similarity NPC61503
0.6933 Remote Similarity NPC129630
0.6923 Remote Similarity NPC329626
0.6923 Remote Similarity NPC470766
0.6905 Remote Similarity NPC125399
0.6905 Remote Similarity NPC255143
0.6905 Remote Similarity NPC281316
0.6892 Remote Similarity NPC276616
0.6857 Remote Similarity NPC40206
0.6849 Remote Similarity NPC473929
0.6849 Remote Similarity NPC267027
0.6849 Remote Similarity NPC475897
0.6829 Remote Similarity NPC145963
0.6818 Remote Similarity NPC161473
0.6806 Remote Similarity NPC140233
0.6806 Remote Similarity NPC287744
0.6806 Remote Similarity NPC144650
0.68 Remote Similarity NPC16964
0.6795 Remote Similarity NPC12696
0.679 Remote Similarity NPC474592
0.6774 Remote Similarity NPC87439
0.6765 Remote Similarity NPC24443
0.6765 Remote Similarity NPC210316
0.6761 Remote Similarity NPC172622
0.6757 Remote Similarity NPC259299
0.6757 Remote Similarity NPC253303
0.6757 Remote Similarity NPC269077
0.6757 Remote Similarity NPC139207
0.6757 Remote Similarity NPC185874
0.6753 Remote Similarity NPC95165
0.6747 Remote Similarity NPC477978
0.6747 Remote Similarity NPC231601
0.6712 Remote Similarity NPC172613
0.6712 Remote Similarity NPC300442
0.6712 Remote Similarity NPC282619
0.6712 Remote Similarity NPC60837
0.6712 Remote Similarity NPC208198
0.6712 Remote Similarity NPC2728
0.6712 Remote Similarity NPC250836
0.6712 Remote Similarity NPC11555
0.6712 Remote Similarity NPC258595
0.6711 Remote Similarity NPC283316
0.6711 Remote Similarity NPC133873
0.6709 Remote Similarity NPC476606
0.6709 Remote Similarity NPC472472
0.6709 Remote Similarity NPC476607
0.6707 Remote Similarity NPC474894
0.6707 Remote Similarity NPC118116
0.6667 Remote Similarity NPC233295
0.6667 Remote Similarity NPC144995
0.6667 Remote Similarity NPC227814
0.6667 Remote Similarity NPC476701
0.6667 Remote Similarity NPC52012
0.6667 Remote Similarity NPC71152
0.6667 Remote Similarity NPC49783
0.6667 Remote Similarity NPC167527
0.6667 Remote Similarity NPC305698
0.6667 Remote Similarity NPC245795
0.6625 Remote Similarity NPC471454
0.6625 Remote Similarity NPC40049
0.6623 Remote Similarity NPC41886
0.6623 Remote Similarity NPC40327
0.6622 Remote Similarity NPC476406
0.662 Remote Similarity NPC469694
0.6618 Remote Similarity NPC223604
0.6618 Remote Similarity NPC84824
0.6618 Remote Similarity NPC67508
0.6582 Remote Similarity NPC476605
0.6579 Remote Similarity NPC74722
0.6579 Remote Similarity NPC473893
0.6579 Remote Similarity NPC304690
0.6579 Remote Similarity NPC9942
0.6579 Remote Similarity NPC329656
0.6579 Remote Similarity NPC474248
0.6575 Remote Similarity NPC300593
0.6575 Remote Similarity NPC68656
0.6575 Remote Similarity NPC476702
0.6575 Remote Similarity NPC309300
0.6575 Remote Similarity NPC225415
0.6567 Remote Similarity NPC165755
0.6548 Remote Similarity NPC239308
0.6543 Remote Similarity NPC321180
0.6533 Remote Similarity NPC477791
0.6533 Remote Similarity NPC193029
0.6533 Remote Similarity NPC473357
0.6533 Remote Similarity NPC472255
0.6533 Remote Similarity NPC136813
0.6533 Remote Similarity NPC472253
0.6528 Remote Similarity NPC15152
0.6528 Remote Similarity NPC475251
0.6522 Remote Similarity NPC264779
0.6522 Remote Similarity NPC39068
0.6517 Remote Similarity NPC262870
0.6506 Remote Similarity NPC246621
0.65 Remote Similarity NPC310643
0.65 Remote Similarity NPC268111
0.65 Remote Similarity NPC126969
0.65 Remote Similarity NPC315261
0.65 Remote Similarity NPC91573
0.6486 Remote Similarity NPC165069
0.6486 Remote Similarity NPC477009
0.6486 Remote Similarity NPC238352
0.6479 Remote Similarity NPC99480
0.6479 Remote Similarity NPC475931
0.6479 Remote Similarity NPC184049
0.6471 Remote Similarity NPC86238
0.6463 Remote Similarity NPC325869
0.6447 Remote Similarity NPC266578
0.6444 Remote Similarity NPC119379
0.6438 Remote Similarity NPC211291
0.6438 Remote Similarity NPC133368
0.6437 Remote Similarity NPC474765
0.6437 Remote Similarity NPC469322
0.6429 Remote Similarity NPC472465
0.6429 Remote Similarity NPC474577
0.642 Remote Similarity NPC477924
0.642 Remote Similarity NPC469867
0.642 Remote Similarity NPC211279
0.642 Remote Similarity NPC283619
0.641 Remote Similarity NPC471271
0.641 Remote Similarity NPC306085
0.641 Remote Similarity NPC164022
0.641 Remote Similarity NPC471268
0.641 Remote Similarity NPC167706
0.641 Remote Similarity NPC471662
0.641 Remote Similarity NPC242992
0.6404 Remote Similarity NPC197107
0.6404 Remote Similarity NPC472466
0.64 Remote Similarity NPC311736
0.64 Remote Similarity NPC250977
0.64 Remote Similarity NPC272125
0.64 Remote Similarity NPC326310
0.6395 Remote Similarity NPC290731
0.6395 Remote Similarity NPC196911
0.6395 Remote Similarity NPC474189
0.6395 Remote Similarity NPC471379
0.6395 Remote Similarity NPC474349
0.6389 Remote Similarity NPC66020
0.6389 Remote Similarity NPC162109
0.6386 Remote Similarity NPC103634
0.6377 Remote Similarity NPC281590
0.6377 Remote Similarity NPC227135
0.6375 Remote Similarity NPC114236
0.6375 Remote Similarity NPC477923
0.6375 Remote Similarity NPC66566
0.6375 Remote Similarity NPC113639
0.6375 Remote Similarity NPC93213
0.6374 Remote Similarity NPC67831
0.6374 Remote Similarity NPC174051
0.6364 Remote Similarity NPC471560
0.6364 Remote Similarity NPC476707
0.6364 Remote Similarity NPC476704
0.6364 Remote Similarity NPC476706
0.6364 Remote Similarity NPC234511
0.6364 Remote Similarity NPC473436
0.6364 Remote Similarity NPC319030
0.6353 Remote Similarity NPC471340
0.6353 Remote Similarity NPC23748
0.6353 Remote Similarity NPC49208
0.6353 Remote Similarity NPC185605
0.6353 Remote Similarity NPC132635
0.6351 Remote Similarity NPC290367
0.6351 Remote Similarity NPC107540
0.6341 Remote Similarity NPC13823
0.6341 Remote Similarity NPC68119
0.6341 Remote Similarity NPC137587

  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 NPC161612 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
0.65 Remote Similarity NPD6933 Approved
0.6437 Remote Similarity NPD7524 Approved
0.6389 Remote Similarity NPD1145 Discontinued
0.625 Remote Similarity NPD6926 Approved
0.625 Remote Similarity NPD6924 Approved
0.6163 Remote Similarity NPD6695 Phase 3
0.6133 Remote Similarity NPD371 Approved
0.6092 Remote Similarity NPD7338 Clinical (unspecified phase)
0.6081 Remote Similarity NPD368 Approved
0.6071 Remote Similarity NPD7645 Phase 2
0.6 Remote Similarity NPD6931 Approved
0.6 Remote Similarity NPD6930 Phase 2
0.5904 Remote Similarity NPD3701 Clinical (unspecified phase)
0.5889 Remote Similarity NPD7750 Discontinued
0.5882 Remote Similarity NPD6929 Approved
0.587 Remote Similarity NPD7838 Discovery
0.5833 Remote Similarity NPD6932 Approved
0.5814 Remote Similarity NPD7525 Registered
0.5814 Remote Similarity NPD7509 Discontinued
0.5783 Remote Similarity NPD6942 Approved
0.5783 Remote Similarity NPD7339 Approved
0.575 Remote Similarity NPD6922 Approved
0.575 Remote Similarity NPD6923 Approved
0.5735 Remote Similarity NPD9410 Clinical (unspecified phase)
0.5699 Remote Similarity NPD6698 Approved
0.5699 Remote Similarity NPD46 Approved
0.5699 Remote Similarity NPD3168 Discontinued
0.5698 Remote Similarity NPD6683 Phase 2
0.5694 Remote Similarity NPD342 Phase 1
0.5679 Remote Similarity NPD7144 Approved
0.5679 Remote Similarity NPD7143 Approved
0.5672 Remote Similarity NPD385 Approved
0.5672 Remote Similarity NPD384 Approved
0.5667 Remote Similarity NPD6893 Approved
0.5657 Remote Similarity NPD4159 Approved
0.5657 Remote Similarity NPD5344 Discontinued
0.5647 Remote Similarity NPD6925 Approved
0.5647 Remote Similarity NPD5776 Phase 2
0.5641 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5638 Remote Similarity NPD7087 Discontinued
0.5632 Remote Similarity NPD7514 Phase 3
0.5632 Remote Similarity NPD7332 Phase 2
0.5612 Remote Similarity NPD4225 Approved
0.561 Remote Similarity NPD7150 Approved
0.561 Remote Similarity NPD7152 Approved
0.561 Remote Similarity NPD7151 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