Structure

Physi-Chem Properties

Molecular Weight:  272.25
Volume:  329.454
LogP:  6.996
LogD:  4.877
LogS:  -6.008
# Rotatable Bonds:  4
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.516
Synthetic Accessibility Score:  4.236
Fsp3:  0.7
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:  -4.597
MDCK Permeability:  1.236952084582299e-05
Pgp-inhibitor:  0.477
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.989
30% Bioavailability (F30%):  0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.051
Plasma Protein Binding (PPB):  94.98049926757812%
Volume Distribution (VD):  3.397
Pgp-substrate:  3.3802590370178223%

ADMET: Metabolism

CYP1A2-inhibitor:  0.48
CYP1A2-substrate:  0.336
CYP2C19-inhibitor:  0.388
CYP2C19-substrate:  0.867
CYP2C9-inhibitor:  0.386
CYP2C9-substrate:  0.415
CYP2D6-inhibitor:  0.153
CYP2D6-substrate:  0.391
CYP3A4-inhibitor:  0.747
CYP3A4-substrate:  0.29

ADMET: Excretion

Clearance (CL):  16.485
Half-life (T1/2):  0.033

ADMET: Toxicity

hERG Blockers:  0.192
Human Hepatotoxicity (H-HT):  0.815
Drug-inuced Liver Injury (DILI):  0.074
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.023
Maximum Recommended Daily Dose:  0.33
Skin Sensitization:  0.718
Carcinogencity:  0.177
Eye Corrosion:  0.19
Eye Irritation:  0.602
Respiratory Toxicity:  0.168

Download Data

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

  Natural Product: NPC17518

Natural Product ID:  NPC17518
Common Name*:   Lobophytumin D
IUPAC Name:   (3S,4aR,8aR)-5,8a-dimethyl-3-(6-methylhepta-1,5-dien-2-yl)-2,3,4,4a,7,8-hexahydro-1H-naphthalene
Synonyms:   Lobophytumin D
Standard InCHIKey:  MVDYCHZUKVXVBG-SLFFLAALSA-N
Standard InCHI:  InChI=1S/C20H32/c1-15(2)8-6-9-16(3)18-11-13-20(5)12-7-10-17(4)19(20)14-18/h8,10,18-19H,3,6-7,9,11-14H2,1-2,4-5H3/t18-,19-,20+/m0/s1
SMILES:  CC(=CCCC(=C)[C@H]1CC[C@@]2(C)CCC=C(C)[C@@H]2C1)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1835377
PubChem CID:   56598868
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids

*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
NPO18815 Lobophytum cristatum Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[21954851]
NPO18815 Lobophytum cristatum Species Alcyoniidae 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 = 36690.0 nM PMID[545333]
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 35740.0 nM PMID[545333]

☑ 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 NPC17518 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
0.9565 High Similarity NPC22765
0.9348 High Similarity NPC124851
0.9333 High Similarity NPC86683
0.8889 High Similarity NPC192529
0.8824 High Similarity NPC469770
0.8696 High Similarity NPC202189
0.8511 High Similarity NPC13991
0.8511 High Similarity NPC114239
0.8511 High Similarity NPC296337
0.8511 High Similarity NPC241784
0.8462 Intermediate Similarity NPC123194
0.8333 Intermediate Similarity NPC469769
0.8298 Intermediate Similarity NPC248411
0.8261 Intermediate Similarity NPC190232
0.8261 Intermediate Similarity NPC193180
0.8261 Intermediate Similarity NPC105246
0.8148 Intermediate Similarity NPC474528
0.8148 Intermediate Similarity NPC474415
0.8148 Intermediate Similarity NPC475696
0.8043 Intermediate Similarity NPC103290
0.8 Intermediate Similarity NPC17810
0.7885 Intermediate Similarity NPC473728
0.7857 Intermediate Similarity NPC475716
0.7857 Intermediate Similarity NPC474455
0.7857 Intermediate Similarity NPC474454
0.7857 Intermediate Similarity NPC474420
0.7843 Intermediate Similarity NPC200129
0.7818 Intermediate Similarity NPC474457
0.7778 Intermediate Similarity NPC229262
0.7778 Intermediate Similarity NPC139717
0.7778 Intermediate Similarity NPC297643
0.7778 Intermediate Similarity NPC470893
0.7755 Intermediate Similarity NPC49088
0.76 Intermediate Similarity NPC323445
0.7586 Intermediate Similarity NPC469728
0.7556 Intermediate Similarity NPC34764
0.7556 Intermediate Similarity NPC190810
0.7556 Intermediate Similarity NPC76145
0.75 Intermediate Similarity NPC177470
0.75 Intermediate Similarity NPC11130
0.7447 Intermediate Similarity NPC62086
0.7447 Intermediate Similarity NPC227632
0.7447 Intermediate Similarity NPC78551
0.7414 Intermediate Similarity NPC311809
0.7414 Intermediate Similarity NPC176621
0.7407 Intermediate Similarity NPC127944
0.7377 Intermediate Similarity NPC279434
0.7377 Intermediate Similarity NPC476039
0.7377 Intermediate Similarity NPC259156
0.7377 Intermediate Similarity NPC242945
0.7377 Intermediate Similarity NPC222366
0.7377 Intermediate Similarity NPC286669
0.7368 Intermediate Similarity NPC60772
0.7347 Intermediate Similarity NPC86538
0.7347 Intermediate Similarity NPC60556
0.7347 Intermediate Similarity NPC109813
0.7333 Intermediate Similarity NPC469662
0.7333 Intermediate Similarity NPC92224
0.7292 Intermediate Similarity NPC144023
0.7288 Intermediate Similarity NPC60565
0.7258 Intermediate Similarity NPC197805
0.7258 Intermediate Similarity NPC176107
0.7213 Intermediate Similarity NPC163678
0.7193 Intermediate Similarity NPC470370
0.7193 Intermediate Similarity NPC470369
0.717 Intermediate Similarity NPC476681
0.7167 Intermediate Similarity NPC283247
0.7167 Intermediate Similarity NPC474086
0.7167 Intermediate Similarity NPC202118
0.7167 Intermediate Similarity NPC197238
0.7143 Intermediate Similarity NPC142754
0.7143 Intermediate Similarity NPC296697
0.7143 Intermediate Similarity NPC82477
0.7143 Intermediate Similarity NPC208999
0.7143 Intermediate Similarity NPC20610
0.7143 Intermediate Similarity NPC216460
0.7143 Intermediate Similarity NPC39157
0.7143 Intermediate Similarity NPC476945
0.7119 Intermediate Similarity NPC127582
0.7097 Intermediate Similarity NPC92327
0.7097 Intermediate Similarity NPC176171
0.7091 Intermediate Similarity NPC474416
0.7091 Intermediate Similarity NPC476679
0.7083 Intermediate Similarity NPC183670
0.7049 Intermediate Similarity NPC285371
0.7049 Intermediate Similarity NPC475124
0.7031 Intermediate Similarity NPC182815
0.7031 Intermediate Similarity NPC286814
0.7021 Intermediate Similarity NPC239039
0.7021 Intermediate Similarity NPC266298
0.7 Intermediate Similarity NPC219621
0.6984 Remote Similarity NPC193770
0.6984 Remote Similarity NPC220210
0.6984 Remote Similarity NPC20181
0.6964 Remote Similarity NPC5626
0.6949 Remote Similarity NPC276764
0.6949 Remote Similarity NPC472827
0.6949 Remote Similarity NPC472304
0.6935 Remote Similarity NPC107258
0.6923 Remote Similarity NPC282593
0.6923 Remote Similarity NPC475728
0.6923 Remote Similarity NPC34834
0.6923 Remote Similarity NPC35734
0.6923 Remote Similarity NPC159577
0.6885 Remote Similarity NPC145715
0.6875 Remote Similarity NPC160209
0.6875 Remote Similarity NPC188292
0.6875 Remote Similarity NPC32055
0.6875 Remote Similarity NPC260474
0.6875 Remote Similarity NPC94192
0.6875 Remote Similarity NPC310992
0.6833 Remote Similarity NPC317778
0.6825 Remote Similarity NPC250977
0.6825 Remote Similarity NPC185587
0.6825 Remote Similarity NPC149680
0.6825 Remote Similarity NPC323005
0.6818 Remote Similarity NPC160817
0.6818 Remote Similarity NPC21773
0.6818 Remote Similarity NPC115023
0.6818 Remote Similarity NPC190035
0.6818 Remote Similarity NPC265789
0.6818 Remote Similarity NPC470078
0.68 Remote Similarity NPC473912
0.6786 Remote Similarity NPC23117
0.6786 Remote Similarity NPC14002
0.678 Remote Similarity NPC27610
0.678 Remote Similarity NPC56905
0.6774 Remote Similarity NPC329698
0.6774 Remote Similarity NPC290367
0.6774 Remote Similarity NPC473959
0.6774 Remote Similarity NPC52449
0.6774 Remote Similarity NPC169275
0.6769 Remote Similarity NPC139397
0.6769 Remote Similarity NPC476431
0.6769 Remote Similarity NPC184919
0.6769 Remote Similarity NPC256846
0.6769 Remote Similarity NPC138409
0.6724 Remote Similarity NPC179024
0.6721 Remote Similarity NPC79576
0.6721 Remote Similarity NPC194208
0.6721 Remote Similarity NPC282694
0.6719 Remote Similarity NPC114651
0.6719 Remote Similarity NPC290350
0.6719 Remote Similarity NPC69649
0.6719 Remote Similarity NPC68703
0.6719 Remote Similarity NPC4370
0.6719 Remote Similarity NPC171225
0.6716 Remote Similarity NPC474228
0.6716 Remote Similarity NPC471799
0.6716 Remote Similarity NPC474488
0.6716 Remote Similarity NPC474140
0.6716 Remote Similarity NPC470044
0.6716 Remote Similarity NPC303613
0.6716 Remote Similarity NPC251705
0.6716 Remote Similarity NPC470045
0.6716 Remote Similarity NPC182717
0.6667 Remote Similarity NPC476683
0.6667 Remote Similarity NPC214770
0.6667 Remote Similarity NPC227670
0.6667 Remote Similarity NPC268039
0.6667 Remote Similarity NPC145498
0.6667 Remote Similarity NPC213749
0.6667 Remote Similarity NPC260040
0.6667 Remote Similarity NPC141777
0.6667 Remote Similarity NPC309825
0.6667 Remote Similarity NPC251929
0.6667 Remote Similarity NPC2634
0.6667 Remote Similarity NPC48638
0.6667 Remote Similarity NPC45727
0.6667 Remote Similarity NPC251118
0.6667 Remote Similarity NPC477856
0.6667 Remote Similarity NPC307176
0.6667 Remote Similarity NPC265782
0.6667 Remote Similarity NPC166362
0.6618 Remote Similarity NPC128346
0.6618 Remote Similarity NPC471797
0.6618 Remote Similarity NPC219232
0.6618 Remote Similarity NPC211641
0.6618 Remote Similarity NPC100334
0.6618 Remote Similarity NPC476904
0.6615 Remote Similarity NPC155198
0.6615 Remote Similarity NPC87141
0.6613 Remote Similarity NPC81615
0.6613 Remote Similarity NPC174956
0.6607 Remote Similarity NPC306195
0.6607 Remote Similarity NPC179169
0.6607 Remote Similarity NPC157781
0.6607 Remote Similarity NPC35519
0.6607 Remote Similarity NPC181255
0.66 Remote Similarity NPC120926
0.66 Remote Similarity NPC218918
0.6567 Remote Similarity NPC225467
0.6567 Remote Similarity NPC242001
0.6567 Remote Similarity NPC234707
0.6567 Remote Similarity NPC110799
0.6567 Remote Similarity NPC54123
0.6567 Remote Similarity NPC167706
0.6562 Remote Similarity NPC37792
0.6557 Remote Similarity NPC135648
0.6552 Remote Similarity NPC200258

  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 NPC17518 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
0.8261 Intermediate Similarity NPD1799 Clinical (unspecified phase)
0.8 Intermediate Similarity NPD8262 Approved
0.7556 Intermediate Similarity NPD319 Phase 1
0.6923 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6923 Remote Similarity NPD6939 Phase 2
0.6875 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6818 Remote Similarity NPD4243 Approved
0.6769 Remote Similarity NPD4137 Phase 3
0.6667 Remote Similarity NPD4747 Approved
0.6667 Remote Similarity NPD4691 Approved
0.6618 Remote Similarity NPD4784 Approved
0.6618 Remote Similarity NPD5733 Approved
0.6618 Remote Similarity NPD4785 Approved
0.6522 Remote Similarity NPD6942 Approved
0.6522 Remote Similarity NPD7339 Approved
0.65 Remote Similarity NPD287 Approved
0.6441 Remote Similarity NPD4219 Approved
0.6377 Remote Similarity NPD4687 Approved
0.6377 Remote Similarity NPD4058 Approved
0.6324 Remote Similarity NPD5276 Approved
0.6286 Remote Similarity NPD5275 Approved
0.6286 Remote Similarity NPD4190 Phase 3
0.6269 Remote Similarity NPD6922 Approved
0.6269 Remote Similarity NPD6923 Approved
0.6197 Remote Similarity NPD3701 Clinical (unspecified phase)
0.6176 Remote Similarity NPD7143 Approved
0.6176 Remote Similarity NPD7144 Approved
0.6164 Remote Similarity NPD7645 Phase 2
0.6087 Remote Similarity NPD7152 Approved
0.6087 Remote Similarity NPD7150 Approved
0.6087 Remote Similarity NPD7151 Approved
0.6056 Remote Similarity NPD8264 Approved
0.6 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5946 Remote Similarity NPD4195 Approved
0.5938 Remote Similarity NPD4194 Approved
0.5938 Remote Similarity NPD4193 Approved
0.5938 Remote Similarity NPD4192 Approved
0.5938 Remote Similarity NPD4191 Approved
0.5915 Remote Similarity NPD6924 Approved
0.5915 Remote Similarity NPD6926 Approved
0.5867 Remote Similarity NPD7525 Registered
0.5789 Remote Similarity NPD8028 Phase 2
0.5769 Remote Similarity NPD4786 Approved
0.5753 Remote Similarity NPD6933 Approved
0.5714 Remote Similarity NPD4223 Phase 3
0.5714 Remote Similarity NPD3667 Approved
0.5714 Remote Similarity NPD4221 Approved
0.5696 Remote Similarity NPD5329 Approved
0.5676 Remote Similarity NPD6925 Approved
0.5676 Remote Similarity NPD5776 Phase 2
0.5676 Remote Similarity NPD6932 Approved
0.5658 Remote Similarity NPD4695 Discontinued
0.5641 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5625 Remote Similarity NPD7521 Approved
0.5625 Remote Similarity NPD7334 Approved
0.5625 Remote Similarity NPD6684 Approved
0.5625 Remote Similarity NPD6098 Approved
0.5625 Remote Similarity NPD6409 Approved
0.5625 Remote Similarity NPD7146 Approved
0.5625 Remote Similarity NPD5330 Approved
0.56 Remote Similarity NPD7145 Approved
0.56 Remote Similarity NPD7322 Clinical (unspecified phase)

  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