Structure

Physi-Chem Properties

Molecular Weight:  502.26
Volume:  536.801
LogP:  4.764
LogD:  5.14
LogS:  -3.674
# Rotatable Bonds:  19
TPSA:  127.2
# H-Bond Aceptor:  8
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.152
Synthetic Accessibility Score:  3.261
Fsp3:  0.429
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.427
MDCK Permeability:  1.8836142771760933e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.988
Human Intestinal Absorption (HIA):  0.937
20% Bioavailability (F20%):  0.872
30% Bioavailability (F30%):  0.976

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.003
Plasma Protein Binding (PPB):  83.54767608642578%
Volume Distribution (VD):  0.616
Pgp-substrate:  2.933140277862549%

ADMET: Metabolism

CYP1A2-inhibitor:  0.322
CYP1A2-substrate:  0.034
CYP2C19-inhibitor:  0.045
CYP2C19-substrate:  0.034
CYP2C9-inhibitor:  0.847
CYP2C9-substrate:  0.997
CYP2D6-inhibitor:  0.861
CYP2D6-substrate:  0.139
CYP3A4-inhibitor:  0.143
CYP3A4-substrate:  0.021

ADMET: Excretion

Clearance (CL):  1.382
Half-life (T1/2):  0.891

ADMET: Toxicity

hERG Blockers:  0.0
Human Hepatotoxicity (H-HT):  0.733
Drug-inuced Liver Injury (DILI):  0.014
AMES Toxicity:  0.001
Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.546
Skin Sensitization:  0.992
Carcinogencity:  0.012
Eye Corrosion:  0.894
Eye Irritation:  0.819
Respiratory Toxicity:  0.202

Download Data

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

  Natural Product: NPC294938

Natural Product ID:  NPC294938
Common Name*:   Cavipetin B
IUPAC Name:   (E)-4-[(2E,6E,10E,14E)-16-[(E)-3-carboxyprop-2-enoyl]oxy-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]-4-oxobut-2-enoic acid
Synonyms:  
Standard InCHIKey:  AHOSPPOAEYRVLQ-WQNLBOQCSA-N
Standard InCHI:  InChI=1S/C28H38O8/c1-21(10-6-12-23(3)18-19-35-27(33)16-14-25(29)30)8-5-9-22(2)11-7-13-24(4)20-36-28(34)17-15-26(31)32/h9-10,13-18H,5-8,11-12,19-20H2,1-4H3,(H,29,30)(H,31,32)/b16-14+,17-15+,21-10+,22-9+,23-18+,24-13+
SMILES:  C/C(=CCC/C(=C/COC(=O)/C=C/C(=O)O)/C)/CC/C=C(C)/CC/C=C(C)/COC(=O)/C=C/C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL469857
PubChem CID:   11237396
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
NPO28298 Boletinus cavipes Species Gyrodontaceae Eukaryota n.a. n.a. n.a. PMID[15217273]
NPO28298 Boletinus cavipes Species Gyrodontaceae 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
NPT2 Others Unspecified Inhibition = 6.0 % PMID[538518]
NPT27 Others Unspecified Activity = 5.0 % PMID[538518]
NPT27 Others Unspecified Activity = 0.0 % PMID[538518]
NPT967 Individual Protein Xanthine dehydrogenase Homo sapiens Inhibition = -1.0 % PMID[538518]
NPT967 Individual Protein Xanthine dehydrogenase Homo sapiens Inhibition = 7.0 % PMID[538518]

☑ 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 NPC294938 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
0.963 High Similarity NPC129150
0.9455 High Similarity NPC223679
0.9455 High Similarity NPC254095
0.9286 High Similarity NPC82465
0.9273 High Similarity NPC249850
0.9273 High Similarity NPC293437
0.9107 High Similarity NPC21946
0.8929 High Similarity NPC135863
0.8333 Intermediate Similarity NPC236338
0.8197 Intermediate Similarity NPC68110
0.8113 Intermediate Similarity NPC308331
0.8113 Intermediate Similarity NPC128280
0.8113 Intermediate Similarity NPC197467
0.8033 Intermediate Similarity NPC26810
0.8 Intermediate Similarity NPC15789
0.7937 Intermediate Similarity NPC282760
0.7925 Intermediate Similarity NPC26600
0.7925 Intermediate Similarity NPC47946
0.7925 Intermediate Similarity NPC270706
0.7869 Intermediate Similarity NPC79756
0.7812 Intermediate Similarity NPC146811
0.7761 Intermediate Similarity NPC316185
0.7742 Intermediate Similarity NPC55376
0.7736 Intermediate Similarity NPC6963
0.7736 Intermediate Similarity NPC304079
0.7727 Intermediate Similarity NPC151481
0.7705 Intermediate Similarity NPC97570
0.7656 Intermediate Similarity NPC273600
0.7619 Intermediate Similarity NPC473737
0.7544 Intermediate Similarity NPC43053
0.7541 Intermediate Similarity NPC474084
0.7536 Intermediate Similarity NPC315843
0.75 Intermediate Similarity NPC135698
0.75 Intermediate Similarity NPC293114
0.7458 Intermediate Similarity NPC478120
0.7391 Intermediate Similarity NPC284006
0.7385 Intermediate Similarity NPC96414
0.7385 Intermediate Similarity NPC19769
0.7377 Intermediate Similarity NPC265551
0.7377 Intermediate Similarity NPC283502
0.7377 Intermediate Similarity NPC212730
0.7358 Intermediate Similarity NPC41409
0.7358 Intermediate Similarity NPC57923
0.7353 Intermediate Similarity NPC476037
0.7353 Intermediate Similarity NPC59558
0.7344 Intermediate Similarity NPC179087
0.7344 Intermediate Similarity NPC210303
0.7344 Intermediate Similarity NPC44343
0.7324 Intermediate Similarity NPC203277
0.7302 Intermediate Similarity NPC98519
0.7302 Intermediate Similarity NPC26223
0.7302 Intermediate Similarity NPC130953
0.7302 Intermediate Similarity NPC471278
0.7288 Intermediate Similarity NPC477780
0.7288 Intermediate Similarity NPC477781
0.7286 Intermediate Similarity NPC107654
0.7273 Intermediate Similarity NPC475555
0.7273 Intermediate Similarity NPC201356
0.7273 Intermediate Similarity NPC475675
0.7258 Intermediate Similarity NPC189700
0.7231 Intermediate Similarity NPC148233
0.7231 Intermediate Similarity NPC25747
0.7231 Intermediate Similarity NPC470808
0.7213 Intermediate Similarity NPC245002
0.7213 Intermediate Similarity NPC96663
0.7188 Intermediate Similarity NPC151648
0.717 Intermediate Similarity NPC221250
0.7167 Intermediate Similarity NPC474127
0.7167 Intermediate Similarity NPC159535
0.7167 Intermediate Similarity NPC151761
0.7164 Intermediate Similarity NPC122627
0.7164 Intermediate Similarity NPC203335
0.7143 Intermediate Similarity NPC302564
0.7143 Intermediate Similarity NPC329890
0.7123 Intermediate Similarity NPC279532
0.7121 Intermediate Similarity NPC471565
0.7121 Intermediate Similarity NPC470123
0.7121 Intermediate Similarity NPC471566
0.7119 Intermediate Similarity NPC106531
0.7101 Intermediate Similarity NPC476012
0.7097 Intermediate Similarity NPC471279
0.7097 Intermediate Similarity NPC471277
0.7091 Intermediate Similarity NPC12907
0.7077 Intermediate Similarity NPC2328
0.7069 Intermediate Similarity NPC275316
0.7049 Intermediate Similarity NPC474913
0.7049 Intermediate Similarity NPC478117
0.7042 Intermediate Similarity NPC470686
0.7015 Intermediate Similarity NPC248125
0.7015 Intermediate Similarity NPC124586
0.6981 Remote Similarity NPC281043
0.6981 Remote Similarity NPC8270
0.697 Remote Similarity NPC308457
0.6964 Remote Similarity NPC160628
0.6957 Remote Similarity NPC475982
0.6944 Remote Similarity NPC260396
0.6944 Remote Similarity NPC285840
0.6944 Remote Similarity NPC327041
0.6935 Remote Similarity NPC221763
0.6935 Remote Similarity NPC51846
0.6935 Remote Similarity NPC324224
0.6935 Remote Similarity NPC150717
0.6935 Remote Similarity NPC472808
0.6912 Remote Similarity NPC478097
0.6912 Remote Similarity NPC225272
0.6912 Remote Similarity NPC132286
0.6909 Remote Similarity NPC116934
0.6901 Remote Similarity NPC185186
0.6901 Remote Similarity NPC327383
0.6901 Remote Similarity NPC329914
0.6901 Remote Similarity NPC474705
0.6897 Remote Similarity NPC15912
0.6892 Remote Similarity NPC473471
0.6885 Remote Similarity NPC269615
0.6885 Remote Similarity NPC218486
0.6875 Remote Similarity NPC286189
0.6875 Remote Similarity NPC222852
0.6875 Remote Similarity NPC22897
0.6875 Remote Similarity NPC159650
0.6866 Remote Similarity NPC478099
0.6866 Remote Similarity NPC478098
0.6866 Remote Similarity NPC471556
0.6857 Remote Similarity NPC202011
0.6857 Remote Similarity NPC329904
0.6857 Remote Similarity NPC469660
0.6857 Remote Similarity NPC4299
0.6857 Remote Similarity NPC473361
0.6852 Remote Similarity NPC269823
0.6849 Remote Similarity NPC205615
0.6849 Remote Similarity NPC188860
0.6849 Remote Similarity NPC16279
0.6849 Remote Similarity NPC469880
0.6849 Remote Similarity NPC256640
0.6849 Remote Similarity NPC477202
0.6842 Remote Similarity NPC315731
0.6825 Remote Similarity NPC472445
0.6825 Remote Similarity NPC268185
0.6825 Remote Similarity NPC44542
0.6818 Remote Similarity NPC155849
0.6818 Remote Similarity NPC217940
0.6818 Remote Similarity NPC475073
0.6812 Remote Similarity NPC63873
0.6812 Remote Similarity NPC474823
0.6812 Remote Similarity NPC218477
0.6812 Remote Similarity NPC238223
0.6812 Remote Similarity NPC475760
0.6806 Remote Similarity NPC114727
0.6806 Remote Similarity NPC476590
0.68 Remote Similarity NPC180725
0.6792 Remote Similarity NPC298413
0.6786 Remote Similarity NPC138935
0.678 Remote Similarity NPC221467
0.678 Remote Similarity NPC27264
0.6769 Remote Similarity NPC299730
0.6769 Remote Similarity NPC309408
0.6765 Remote Similarity NPC37382
0.6765 Remote Similarity NPC478101
0.6765 Remote Similarity NPC276299
0.6761 Remote Similarity NPC477087
0.6761 Remote Similarity NPC84038
0.6761 Remote Similarity NPC477086
0.6757 Remote Similarity NPC477203
0.6757 Remote Similarity NPC51809
0.6757 Remote Similarity NPC49302
0.6757 Remote Similarity NPC233071
0.6757 Remote Similarity NPC474818
0.6757 Remote Similarity NPC176329
0.6757 Remote Similarity NPC125365
0.6727 Remote Similarity NPC256766
0.6727 Remote Similarity NPC213538
0.6719 Remote Similarity NPC471619
0.6716 Remote Similarity NPC34883
0.6716 Remote Similarity NPC226066
0.6714 Remote Similarity NPC476591
0.6714 Remote Similarity NPC101622
0.6714 Remote Similarity NPC475004
0.6714 Remote Similarity NPC88877
0.6714 Remote Similarity NPC470693
0.6712 Remote Similarity NPC478195
0.6712 Remote Similarity NPC478192
0.6712 Remote Similarity NPC478196
0.6712 Remote Similarity NPC478193
0.6712 Remote Similarity NPC478194
0.6712 Remote Similarity NPC478191
0.6711 Remote Similarity NPC470147
0.6711 Remote Similarity NPC133226
0.6667 Remote Similarity NPC148056
0.6667 Remote Similarity NPC230296
0.6667 Remote Similarity NPC209135
0.6667 Remote Similarity NPC474816
0.6667 Remote Similarity NPC140501
0.6667 Remote Similarity NPC248775
0.6667 Remote Similarity NPC66460
0.6667 Remote Similarity NPC221095
0.6667 Remote Similarity NPC472266
0.6667 Remote Similarity NPC287878
0.6667 Remote Similarity NPC477314
0.6667 Remote Similarity NPC478100
0.6667 Remote Similarity NPC316851
0.6667 Remote Similarity NPC108816

  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 NPC294938 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
0.7857 Intermediate Similarity NPD6927 Phase 3
0.7818 Intermediate Similarity NPD4220 Pre-registration
0.6786 Remote Similarity NPD6096 Approved
0.6786 Remote Similarity NPD6097 Approved
0.6724 Remote Similarity NPD5343 Approved
0.6716 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6667 Remote Similarity NPD4265 Approved
0.6618 Remote Similarity NPD2685 Clinical (unspecified phase)
0.65 Remote Similarity NPD2268 Discontinued
0.6418 Remote Similarity NPD4191 Approved
0.6418 Remote Similarity NPD4192 Approved
0.6418 Remote Similarity NPD4194 Approved
0.6418 Remote Similarity NPD4193 Approved
0.6415 Remote Similarity NPD9115 Approved
0.6379 Remote Similarity NPD39 Approved
0.6316 Remote Similarity NPD5326 Phase 3
0.6316 Remote Similarity NPD9411 Phase 1
0.6269 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6212 Remote Similarity NPD6109 Phase 1
0.6173 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6118 Remote Similarity NPD7838 Discovery
0.6102 Remote Similarity NPD4222 Approved
0.5972 Remote Similarity NPD4247 Clinical (unspecified phase)
0.597 Remote Similarity NPD585 Clinical (unspecified phase)
0.5926 Remote Similarity NPD5209 Approved
0.5897 Remote Similarity NPD4756 Discovery
0.5849 Remote Similarity NPD8573 Approved
0.5844 Remote Similarity NPD8039 Approved
0.5844 Remote Similarity NPD1452 Discontinued
0.5824 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5806 Remote Similarity NPD3173 Approved
0.5747 Remote Similarity NPD6698 Approved
0.5747 Remote Similarity NPD5785 Approved
0.5747 Remote Similarity NPD46 Approved
0.5732 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5714 Remote Similarity NPD9418 Clinical (unspecified phase)
0.5679 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5663 Remote Similarity NPD7154 Phase 3
0.5614 Remote Similarity NPD5783 Phase 3
0.5606 Remote Similarity NPD3196 Approved
0.5606 Remote Similarity NPD3195 Phase 2
0.5606 Remote Similarity NPD4266 Approved
0.5606 Remote Similarity NPD3194 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