Structure

Physi-Chem Properties

Molecular Weight:  320.1
Volume:  325.763
LogP:  3.333
LogD:  3.083
LogS:  -3.787
# Rotatable Bonds:  0
TPSA:  58.92
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  5
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.657
Synthetic Accessibility Score:  3.785
Fsp3:  0.2
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:  -5.001
MDCK Permeability:  1.8885015379055403e-05
Pgp-inhibitor:  0.024
Pgp-substrate:  0.257
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.065
30% Bioavailability (F30%):  0.674

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.506
Plasma Protein Binding (PPB):  97.54271697998047%
Volume Distribution (VD):  0.747
Pgp-substrate:  1.99427330493927%

ADMET: Metabolism

CYP1A2-inhibitor:  0.822
CYP1A2-substrate:  0.471
CYP2C19-inhibitor:  0.9
CYP2C19-substrate:  0.363
CYP2C9-inhibitor:  0.9
CYP2C9-substrate:  0.944
CYP2D6-inhibitor:  0.717
CYP2D6-substrate:  0.329
CYP3A4-inhibitor:  0.686
CYP3A4-substrate:  0.606

ADMET: Excretion

Clearance (CL):  8.167
Half-life (T1/2):  0.731

ADMET: Toxicity

hERG Blockers:  0.043
Human Hepatotoxicity (H-HT):  0.296
Drug-inuced Liver Injury (DILI):  0.284
AMES Toxicity:  0.946
Rat Oral Acute Toxicity:  0.737
Maximum Recommended Daily Dose:  0.938
Skin Sensitization:  0.772
Carcinogencity:  0.952
Eye Corrosion:  0.003
Eye Irritation:  0.707
Respiratory Toxicity:  0.931

Download Data

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

  Natural Product: NPC138935

Natural Product ID:  NPC138935
Common Name*:   12,13-Dehydrogeranylgeraniol
IUPAC Name:   (2E,6E,10E,12E)-3,7,11,15-tetramethylhexadeca-2,6,10,12,14-pentaen-1-ol
Synonyms:   12,13-Dehydrogeranylgeraniol
Standard InCHIKey:  OTYIYOOKHMFXBC-UBZGHHIISA-N
Standard InCHI:  InChI=1S/C20H32O/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-21/h6,9-11,13,15,21H,7-8,12,14,16H2,1-5H3/b10-6+,18-11+,19-13+,20-15+
SMILES:  OC/C=C(/CC/C=C(/CC/C=C(/C=C/C=C(C)C)C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL459827
PubChem CID:   10469408
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0001357] Acyclic 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
NPO12012 Saururus cernuus Species Saururaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0040-4039(01)99818-1]
NPO12012 Saururus cernuus Species Saururaceae Eukaryota n.a. n.a. n.a. PMID[11421725]
NPO12012 Saururus cernuus Species Saururaceae Eukaryota n.a. n.a. n.a. PMID[15165135]
NPO12012 Saururus cernuus Species Saururaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12012 Saururus cernuus Species Saururaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24129 Bifurcaria bifurcata Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12012 Saururus cernuus Species Saururaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12012 Saururus cernuus Species Saururaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24129 Bifurcaria bifurcata Species Sargassaceae 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
NPT116 Cell Line HL-60 Homo sapiens Inhibition = 8.0 % PMID[463361]
NPT116 Cell Line HL-60 Homo sapiens Inhibition = 28.0 % PMID[463361]

☑ 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 NPC138935 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
0.9268 High Similarity NPC269823
0.9048 High Similarity NPC256766
0.9048 High Similarity NPC213538
0.8837 High Similarity NPC116934
0.878 High Similarity NPC182840
0.878 High Similarity NPC103213
0.878 High Similarity NPC29091
0.878 High Similarity NPC255042
0.8605 High Similarity NPC206906
0.8444 Intermediate Similarity NPC140501
0.8444 Intermediate Similarity NPC160628
0.8333 Intermediate Similarity NPC15934
0.8261 Intermediate Similarity NPC180575
0.8125 Intermediate Similarity NPC474460
0.7805 Intermediate Similarity NPC58957
0.7778 Intermediate Similarity NPC304151
0.7755 Intermediate Similarity NPC182102
0.7755 Intermediate Similarity NPC328784
0.7755 Intermediate Similarity NPC291437
0.7755 Intermediate Similarity NPC26960
0.7692 Intermediate Similarity NPC329686
0.766 Intermediate Similarity NPC269074
0.76 Intermediate Similarity NPC474495
0.76 Intermediate Similarity NPC59408
0.76 Intermediate Similarity NPC473672
0.76 Intermediate Similarity NPC71053
0.7561 Intermediate Similarity NPC250734
0.7551 Intermediate Similarity NPC267110
0.7547 Intermediate Similarity NPC55412
0.7547 Intermediate Similarity NPC249645
0.7451 Intermediate Similarity NPC208638
0.74 Intermediate Similarity NPC473913
0.74 Intermediate Similarity NPC249670
0.74 Intermediate Similarity NPC474642
0.7308 Intermediate Similarity NPC61177
0.7308 Intermediate Similarity NPC474496
0.7292 Intermediate Similarity NPC276825
0.7273 Intermediate Similarity NPC34873
0.7273 Intermediate Similarity NPC40434
0.72 Intermediate Similarity NPC248884
0.72 Intermediate Similarity NPC31194
0.72 Intermediate Similarity NPC85079
0.72 Intermediate Similarity NPC153538
0.717 Intermediate Similarity NPC110732
0.7143 Intermediate Similarity NPC305759
0.7143 Intermediate Similarity NPC173592
0.7143 Intermediate Similarity NPC124183
0.7143 Intermediate Similarity NPC55063
0.7143 Intermediate Similarity NPC99088
0.7143 Intermediate Similarity NPC35141
0.7143 Intermediate Similarity NPC308331
0.7143 Intermediate Similarity NPC19834
0.7115 Intermediate Similarity NPC35756
0.7091 Intermediate Similarity NPC129150
0.7083 Intermediate Similarity NPC101616
0.7059 Intermediate Similarity NPC199286
0.7059 Intermediate Similarity NPC72699
0.7059 Intermediate Similarity NPC477727
0.7059 Intermediate Similarity NPC471281
0.7037 Intermediate Similarity NPC474644
0.7021 Intermediate Similarity NPC88079
0.7021 Intermediate Similarity NPC68889
0.7021 Intermediate Similarity NPC108494
0.7021 Intermediate Similarity NPC209279
0.7021 Intermediate Similarity NPC67761
0.7021 Intermediate Similarity NPC180871
0.7021 Intermediate Similarity NPC194586
0.7021 Intermediate Similarity NPC51758
0.7 Intermediate Similarity NPC318549
0.6981 Remote Similarity NPC34577
0.6964 Remote Similarity NPC223679
0.6964 Remote Similarity NPC181872
0.6957 Remote Similarity NPC329762
0.6957 Remote Similarity NPC103236
0.6957 Remote Similarity NPC56917
0.6957 Remote Similarity NPC27444
0.6939 Remote Similarity NPC76976
0.6923 Remote Similarity NPC151782
0.6923 Remote Similarity NPC471959
0.6923 Remote Similarity NPC89824
0.6923 Remote Similarity NPC477723
0.6923 Remote Similarity NPC294278
0.6923 Remote Similarity NPC55383
0.6923 Remote Similarity NPC165447
0.6923 Remote Similarity NPC329608
0.6923 Remote Similarity NPC244038
0.6923 Remote Similarity NPC256656
0.6923 Remote Similarity NPC76198
0.6923 Remote Similarity NPC170776
0.6923 Remote Similarity NPC9273
0.6923 Remote Similarity NPC93639
0.6923 Remote Similarity NPC224148
0.6923 Remote Similarity NPC197272
0.6923 Remote Similarity NPC475477
0.6909 Remote Similarity NPC473865
0.6909 Remote Similarity NPC474643
0.6863 Remote Similarity NPC302310
0.6863 Remote Similarity NPC125122
0.6863 Remote Similarity NPC471276
0.6863 Remote Similarity NPC471280
0.6863 Remote Similarity NPC471275
0.6842 Remote Similarity NPC322186
0.6842 Remote Similarity NPC322002
0.6833 Remote Similarity NPC308844
0.6833 Remote Similarity NPC477525
0.6829 Remote Similarity NPC60288
0.6829 Remote Similarity NPC242117
0.6792 Remote Similarity NPC142092
0.6786 Remote Similarity NPC44542
0.6786 Remote Similarity NPC268185
0.6786 Remote Similarity NPC472445
0.6786 Remote Similarity NPC294938
0.6786 Remote Similarity NPC11130
0.6735 Remote Similarity NPC6963
0.6735 Remote Similarity NPC304079
0.6735 Remote Similarity NPC108195
0.6727 Remote Similarity NPC297020
0.6727 Remote Similarity NPC471992
0.6724 Remote Similarity NPC130807
0.6724 Remote Similarity NPC327112
0.6721 Remote Similarity NPC129995
0.6721 Remote Similarity NPC315141
0.6667 Remote Similarity NPC254095
0.6667 Remote Similarity NPC303672
0.6667 Remote Similarity NPC149668
0.6667 Remote Similarity NPC217188
0.6667 Remote Similarity NPC226848
0.6607 Remote Similarity NPC24216
0.6607 Remote Similarity NPC324224
0.6607 Remote Similarity NPC104138
0.6607 Remote Similarity NPC261158
0.6607 Remote Similarity NPC472808
0.6607 Remote Similarity NPC306420
0.6604 Remote Similarity NPC243539
0.6604 Remote Similarity NPC54542
0.6604 Remote Similarity NPC43053
0.6604 Remote Similarity NPC304223
0.6604 Remote Similarity NPC267340
0.6604 Remote Similarity NPC129263
0.6604 Remote Similarity NPC145032
0.66 Remote Similarity NPC210560
0.66 Remote Similarity NPC221379
0.66 Remote Similarity NPC24824
0.66 Remote Similarity NPC165651
0.6585 Remote Similarity NPC138113
0.6585 Remote Similarity NPC123965
0.6585 Remote Similarity NPC115959
0.6557 Remote Similarity NPC7940
0.6552 Remote Similarity NPC82465
0.6552 Remote Similarity NPC122239
0.6552 Remote Similarity NPC475931
0.6545 Remote Similarity NPC256209
0.6545 Remote Similarity NPC49059
0.6545 Remote Similarity NPC48058
0.6545 Remote Similarity NPC189677
0.6545 Remote Similarity NPC473532
0.6531 Remote Similarity NPC252978
0.6512 Remote Similarity NPC63121
0.6512 Remote Similarity NPC197356
0.65 Remote Similarity NPC471023
0.6491 Remote Similarity NPC293437
0.6491 Remote Similarity NPC249850
0.6491 Remote Similarity NPC135863
0.6491 Remote Similarity NPC71755
0.6481 Remote Similarity NPC195986
0.6471 Remote Similarity NPC197467
0.6444 Remote Similarity NPC79544
0.6441 Remote Similarity NPC176621
0.6441 Remote Similarity NPC471081
0.6429 Remote Similarity NPC273023
0.6429 Remote Similarity NPC475353
0.6429 Remote Similarity NPC130209
0.6429 Remote Similarity NPC251666
0.6429 Remote Similarity NPC232247
0.6429 Remote Similarity NPC474513
0.6429 Remote Similarity NPC471991
0.6429 Remote Similarity NPC477726
0.6429 Remote Similarity NPC473721
0.6429 Remote Similarity NPC298299
0.6429 Remote Similarity NPC146551
0.6429 Remote Similarity NPC148216
0.6429 Remote Similarity NPC473725
0.6429 Remote Similarity NPC473896
0.6429 Remote Similarity NPC470963
0.6429 Remote Similarity NPC227135
0.6429 Remote Similarity NPC152668
0.6429 Remote Similarity NPC477725
0.6429 Remote Similarity NPC473910
0.6429 Remote Similarity NPC473735
0.6429 Remote Similarity NPC148163
0.6415 Remote Similarity NPC288381
0.6415 Remote Similarity NPC475071
0.6415 Remote Similarity NPC225974
0.6415 Remote Similarity NPC267692
0.6415 Remote Similarity NPC307435
0.6415 Remote Similarity NPC20934
0.64 Remote Similarity NPC12907
0.6393 Remote Similarity NPC110241
0.6379 Remote Similarity NPC21946
0.6364 Remote Similarity NPC119655

  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 NPC138935 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
0.8444 Intermediate Similarity NPD4265 Approved
0.7551 Intermediate Similarity NPD4220 Pre-registration
0.7547 Intermediate Similarity NPD4219 Approved
0.6724 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6429 Remote Similarity NPD342 Phase 1
0.6415 Remote Similarity NPD2268 Discontinued
0.6383 Remote Similarity NPD5783 Phase 3
0.6296 Remote Similarity NPD6927 Phase 3
0.6094 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6066 Remote Similarity NPD4191 Approved
0.6066 Remote Similarity NPD4194 Approved
0.6066 Remote Similarity NPD4193 Approved
0.6066 Remote Similarity NPD4192 Approved
0.5968 Remote Similarity NPD3210 Clinical (unspecified phase)
0.5962 Remote Similarity NPD39 Approved
0.5942 Remote Similarity NPD8264 Approved
0.5882 Remote Similarity NPD4732 Discontinued
0.5882 Remote Similarity NPD5326 Phase 3
0.5873 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5833 Remote Similarity NPD585 Clinical (unspecified phase)
0.5806 Remote Similarity NPD368 Approved
0.5769 Remote Similarity NPD6097 Approved
0.5769 Remote Similarity NPD6096 Approved
0.5741 Remote Similarity NPD5343 Approved
0.5694 Remote Similarity NPD7322 Clinical (unspecified phase)
0.566 Remote Similarity NPD4222 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