Structure

Physi-Chem Properties

Molecular Weight:  429.29
Volume:  471.478
LogP:  6.41
LogD:  4.474
LogS:  -2.934
# Rotatable Bonds:  11
TPSA:  74.71
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.332
Synthetic Accessibility Score:  4.482
Fsp3:  0.538
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:  -4.905
MDCK Permeability:  1.4699840903631411e-05
Pgp-inhibitor:  0.238
Pgp-substrate:  0.774
Human Intestinal Absorption (HIA):  0.104
20% Bioavailability (F20%):  0.957
30% Bioavailability (F30%):  0.678

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.042
Plasma Protein Binding (PPB):  98.44135284423828%
Volume Distribution (VD):  1.563
Pgp-substrate:  1.9756438732147217%

ADMET: Metabolism

CYP1A2-inhibitor:  0.044
CYP1A2-substrate:  0.248
CYP2C19-inhibitor:  0.167
CYP2C19-substrate:  0.086
CYP2C9-inhibitor:  0.435
CYP2C9-substrate:  0.982
CYP2D6-inhibitor:  0.842
CYP2D6-substrate:  0.661
CYP3A4-inhibitor:  0.42
CYP3A4-substrate:  0.18

ADMET: Excretion

Clearance (CL):  3.81
Half-life (T1/2):  0.217

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.854
Drug-inuced Liver Injury (DILI):  0.822
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.98
Skin Sensitization:  0.905
Carcinogencity:  0.553
Eye Corrosion:  0.003
Eye Irritation:  0.07
Respiratory Toxicity:  0.845

Download Data

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

  Natural Product: NPC121857

Natural Product ID:  NPC121857
Common Name*:   Hippolide B
IUPAC Name:   (3S)-3-[(2R,6S)-6-methoxy-5-[(3E,7E)-4,8,12-trimethyltrideca-3,7,11-trienyl]-3,6-dihydro-2H-pyran-2-yl]pyrrolidine-2,5-dione
Synonyms:   Hippolide B
Standard InCHIKey:  JCZZVHJOSFEULF-UTNVMCOPSA-N
Standard InCHI:  InChI=1S/C26H39NO4/c1-18(2)9-6-10-19(3)11-7-12-20(4)13-8-14-21-15-16-23(31-26(21)30-5)22-17-24(28)27-25(22)29/h9,11,13,15,22-23,26H,6-8,10,12,14,16-17H2,1-5H3,(H,27,28,29)/b19-11+,20-13+/t22-,23+,26-/m0/s1
SMILES:  CC(=CCC/C(=C/CC/C(=C/CCC1=CC[C@H]([C@@H]2CC(=NC2=O)O)O[C@@H]1OC)/C)/C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1784622
PubChem CID:   53262773
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
NPO15322 Hippospongia lachne Species Spongiidae Eukaryota n.a. n.a. n.a. PMID[21548579]
NPO15322 Hippospongia lachne Species Spongiidae 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
NPT178 Individual Protein Protein-tyrosine phosphatase 1B Homo sapiens IC50 = 39670.0 nM PMID[496117]
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 35130.0 nM PMID[496117]

☑ 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 NPC121857 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
0.967 High Similarity NPC167380
0.7182 Intermediate Similarity NPC24389
0.717 Intermediate Similarity NPC175531
0.7064 Intermediate Similarity NPC271269
0.7009 Intermediate Similarity NPC313234
0.6909 Remote Similarity NPC154601
0.6893 Remote Similarity NPC472264
0.6847 Remote Similarity NPC251330
0.6731 Remote Similarity NPC9447
0.6637 Remote Similarity NPC475150
0.6574 Remote Similarity NPC150967
0.6505 Remote Similarity NPC241054
0.6486 Remote Similarity NPC128501
0.6442 Remote Similarity NPC106051
0.6442 Remote Similarity NPC137368
0.6442 Remote Similarity NPC472011
0.6422 Remote Similarity NPC265662
0.6415 Remote Similarity NPC314500
0.641 Remote Similarity NPC469865
0.6393 Remote Similarity NPC469515
0.6389 Remote Similarity NPC150041
0.6381 Remote Similarity NPC471054
0.6372 Remote Similarity NPC14537
0.6364 Remote Similarity NPC321728
0.6364 Remote Similarity NPC234542
0.6336 Remote Similarity NPC230889
0.6333 Remote Similarity NPC316325
0.633 Remote Similarity NPC475503
0.6321 Remote Similarity NPC475879
0.6316 Remote Similarity NPC473252
0.6306 Remote Similarity NPC473224
0.6293 Remote Similarity NPC473578
0.6273 Remote Similarity NPC4834
0.6273 Remote Similarity NPC476344
0.6271 Remote Similarity NPC7797
0.6262 Remote Similarity NPC472010
0.6262 Remote Similarity NPC472199
0.6262 Remote Similarity NPC471059
0.625 Remote Similarity NPC98859
0.625 Remote Similarity NPC4637
0.625 Remote Similarity NPC469483
0.624 Remote Similarity NPC469494
0.6239 Remote Similarity NPC113012
0.6239 Remote Similarity NPC122926
0.6228 Remote Similarity NPC472616
0.6228 Remote Similarity NPC64168
0.6214 Remote Similarity NPC158756
0.6207 Remote Similarity NPC140251
0.6207 Remote Similarity NPC307903
0.6195 Remote Similarity NPC469598
0.6194 Remote Similarity NPC315210
0.6194 Remote Similarity NPC315848
0.619 Remote Similarity NPC45409
0.6186 Remote Similarity NPC316984
0.6186 Remote Similarity NPC170375
0.6186 Remote Similarity NPC30911
0.6182 Remote Similarity NPC306041
0.6182 Remote Similarity NPC54731
0.6174 Remote Similarity NPC472615
0.6174 Remote Similarity NPC475918
0.6168 Remote Similarity NPC475995
0.6168 Remote Similarity NPC474098
0.6154 Remote Similarity NPC470755
0.6154 Remote Similarity NPC163606
0.6148 Remote Similarity NPC296361
0.6147 Remote Similarity NPC472198
0.614 Remote Similarity NPC279833
0.614 Remote Similarity NPC80439
0.614 Remote Similarity NPC474563
0.614 Remote Similarity NPC173690
0.614 Remote Similarity NPC6271
0.6126 Remote Similarity NPC475646
0.6117 Remote Similarity NPC286770
0.6117 Remote Similarity NPC284472
0.6117 Remote Similarity NPC229799
0.6117 Remote Similarity NPC16488
0.6111 Remote Similarity NPC472197
0.6107 Remote Similarity NPC78189
0.6106 Remote Similarity NPC28304
0.6106 Remote Similarity NPC298255
0.6102 Remote Similarity NPC127578
0.61 Remote Similarity NPC127526
0.61 Remote Similarity NPC108816
0.61 Remote Similarity NPC93763
0.6095 Remote Similarity NPC469910
0.6094 Remote Similarity NPC477793
0.6094 Remote Similarity NPC329919
0.6087 Remote Similarity NPC259476
0.6071 Remote Similarity NPC151093
0.6071 Remote Similarity NPC313440
0.6071 Remote Similarity NPC473154
0.6068 Remote Similarity NPC168733
0.6066 Remote Similarity NPC216335
0.6058 Remote Similarity NPC266718
0.6058 Remote Similarity NPC126518
0.6058 Remote Similarity NPC41856
0.6055 Remote Similarity NPC320552
0.6055 Remote Similarity NPC61201
0.6053 Remote Similarity NPC310804
0.6053 Remote Similarity NPC471599
0.6053 Remote Similarity NPC261117
0.6053 Remote Similarity NPC222062
0.6053 Remote Similarity NPC477198
0.605 Remote Similarity NPC29501
0.604 Remote Similarity NPC99651
0.6038 Remote Similarity NPC142583
0.6036 Remote Similarity NPC123141
0.6034 Remote Similarity NPC201128
0.6031 Remote Similarity NPC314361
0.602 Remote Similarity NPC140287
0.6019 Remote Similarity NPC474959
0.6019 Remote Similarity NPC323251
0.6019 Remote Similarity NPC477866
0.6019 Remote Similarity NPC471298
0.6019 Remote Similarity NPC477865
0.6019 Remote Similarity NPC303451
0.6019 Remote Similarity NPC6414
0.6019 Remote Similarity NPC327253
0.6019 Remote Similarity NPC471296
0.6019 Remote Similarity NPC310450
0.6019 Remote Similarity NPC475046
0.6019 Remote Similarity NPC11383
0.6018 Remote Similarity NPC22149
0.6018 Remote Similarity NPC255677
0.6018 Remote Similarity NPC244878
0.6018 Remote Similarity NPC306344
0.6017 Remote Similarity NPC329305
0.6017 Remote Similarity NPC298484
0.6017 Remote Similarity NPC474725
0.6017 Remote Similarity NPC474891
0.6 Remote Similarity NPC118761
0.6 Remote Similarity NPC471060
0.6 Remote Similarity NPC471300
0.6 Remote Similarity NPC55336
0.6 Remote Similarity NPC315915
0.6 Remote Similarity NPC475832
0.6 Remote Similarity NPC320630
0.6 Remote Similarity NPC197541
0.6 Remote Similarity NPC267869
0.6 Remote Similarity NPC475927
0.6 Remote Similarity NPC10572
0.6 Remote Similarity NPC97516
0.6 Remote Similarity NPC474827
0.6 Remote Similarity NPC474828
0.6 Remote Similarity NPC68001
0.6 Remote Similarity NPC116177
0.6 Remote Similarity NPC234304
0.6 Remote Similarity NPC284929
0.6 Remote Similarity NPC470124
0.6 Remote Similarity NPC7563
0.6 Remote Similarity NPC474860
0.6 Remote Similarity NPC199831
0.5984 Remote Similarity NPC7905
0.5984 Remote Similarity NPC315652
0.5984 Remote Similarity NPC204639
0.5983 Remote Similarity NPC315426
0.5983 Remote Similarity NPC475800
0.5983 Remote Similarity NPC474285
0.5983 Remote Similarity NPC254538
0.5982 Remote Similarity NPC471462
0.5982 Remote Similarity NPC52820
0.5982 Remote Similarity NPC475709
0.5981 Remote Similarity NPC471057
0.5981 Remote Similarity NPC471058
0.5981 Remote Similarity NPC476805
0.5981 Remote Similarity NPC475819
0.5981 Remote Similarity NPC476803
0.5979 Remote Similarity NPC126061
0.5966 Remote Similarity NPC92829
0.5965 Remote Similarity NPC219038
0.5965 Remote Similarity NPC20673
0.5963 Remote Similarity NPC141831
0.5962 Remote Similarity NPC131669
0.5962 Remote Similarity NPC473390
0.5962 Remote Similarity NPC169575
0.5962 Remote Similarity NPC40746
0.5962 Remote Similarity NPC471297
0.596 Remote Similarity NPC199445
0.596 Remote Similarity NPC315552
0.596 Remote Similarity NPC329852
0.595 Remote Similarity NPC5485
0.595 Remote Similarity NPC475988
0.5948 Remote Similarity NPC205176
0.5948 Remote Similarity NPC86095
0.5946 Remote Similarity NPC469543
0.5946 Remote Similarity NPC476488
0.5946 Remote Similarity NPC189764
0.5946 Remote Similarity NPC476487
0.5946 Remote Similarity NPC54905
0.5946 Remote Similarity NPC314009
0.5943 Remote Similarity NPC316426
0.5943 Remote Similarity NPC315395
0.5943 Remote Similarity NPC478112
0.5943 Remote Similarity NPC261721
0.5941 Remote Similarity NPC267231
0.594 Remote Similarity NPC472428
0.5938 Remote Similarity NPC101622
0.5935 Remote Similarity NPC147707
0.5932 Remote Similarity NPC476034
0.5932 Remote Similarity NPC474969

  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 NPC121857 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
0.6355 Remote Similarity NPD5781 Clinical (unspecified phase)
0.6333 Remote Similarity NPD7500 Approved
0.633 Remote Similarity NPD4228 Discovery
0.6239 Remote Similarity NPD6420 Discontinued
0.6186 Remote Similarity NPD7601 Clinical (unspecified phase)
0.6186 Remote Similarity NPD2204 Approved
0.6058 Remote Similarity NPD6400 Clinical (unspecified phase)
0.605 Remote Similarity NPD7116 Clinical (unspecified phase)
0.6 Remote Similarity NPD6914 Discontinued
0.5966 Remote Similarity NPD6421 Discontinued
0.5917 Remote Similarity NPD1719 Phase 1
0.5897 Remote Similarity NPD4211 Phase 1
0.5893 Remote Similarity NPD7839 Suspended
0.5891 Remote Similarity NPD8074 Phase 3
0.5882 Remote Similarity NPD6413 Approved
0.5814 Remote Similarity NPD8451 Approved
0.5781 Remote Similarity NPD7642 Approved
0.5769 Remote Similarity NPD8448 Approved
0.5758 Remote Similarity NPD8391 Approved
0.5758 Remote Similarity NPD8392 Approved
0.5758 Remote Similarity NPD8390 Approved
0.5748 Remote Similarity NPD8444 Approved
0.5701 Remote Similarity NPD6082 Clinical (unspecified phase)
0.568 Remote Similarity NPD7505 Discontinued
0.5673 Remote Similarity NPD4252 Approved
0.5673 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5667 Remote Similarity NPD6686 Approved
0.5659 Remote Similarity NPD7829 Approved
0.5659 Remote Similarity NPD7830 Approved
0.5652 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5625 Remote Similarity NPD8513 Phase 3
0.5625 Remote Similarity NPD7739 Clinical (unspecified phase)
0.5615 Remote Similarity NPD8341 Approved
0.5615 Remote Similarity NPD8340 Approved
0.5615 Remote Similarity NPD8342 Approved
0.5615 Remote Similarity NPD8299 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