Structure

Physi-Chem Properties

Molecular Weight:  416.26
Volume:  463.816
LogP:  5.115
LogD:  4.523
LogS:  -4.263
# Rotatable Bonds:  15
TPSA:  80.67
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.165
Synthetic Accessibility Score:  3.35
Fsp3:  0.48
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.2
MDCK Permeability:  4.6903373004170135e-05
Pgp-inhibitor:  0.085
Pgp-substrate:  0.089
Human Intestinal Absorption (HIA):  0.951
20% Bioavailability (F20%):  0.697
30% Bioavailability (F30%):  0.285

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.009
Plasma Protein Binding (PPB):  95.18074798583984%
Volume Distribution (VD):  0.356
Pgp-substrate:  1.1425385475158691%

ADMET: Metabolism

CYP1A2-inhibitor:  0.365
CYP1A2-substrate:  0.243
CYP2C19-inhibitor:  0.316
CYP2C19-substrate:  0.064
CYP2C9-inhibitor:  0.883
CYP2C9-substrate:  0.986
CYP2D6-inhibitor:  0.819
CYP2D6-substrate:  0.237
CYP3A4-inhibitor:  0.092
CYP3A4-substrate:  0.129

ADMET: Excretion

Clearance (CL):  2.274
Half-life (T1/2):  0.837

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.782
Drug-inuced Liver Injury (DILI):  0.006
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.895
Skin Sensitization:  0.986
Carcinogencity:  0.013
Eye Corrosion:  0.874
Eye Irritation:  0.891
Respiratory Toxicity:  0.852

Download Data

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

  Natural Product: NPC21946

Natural Product ID:  NPC21946
Common Name*:   Boletinin I
IUPAC Name:   (E)-3-methyl-4-oxo-4-[(2E,6E,10E,14E)-3,7,11,15-tetramethyl-16-oxohexadeca-2,6,10,14-tetraenoxy]but-2-enoic acid
Synonyms:   Boletinin I
Standard InCHIKey:  AOJDLUWCHJXNCH-SDWHTVMGSA-N
Standard InCHI:  InChI=1S/C25H36O5/c1-19(9-6-10-20(2)12-8-14-22(4)18-26)11-7-13-21(3)15-16-30-25(29)23(5)17-24(27)28/h10-11,14-15,17-18H,6-9,12-13,16H2,1-5H3,(H,27,28)/b19-11+,20-10+,21-15+,22-14+,23-17+
SMILES:  O=C/C(=C/CC/C(=C/CC/C(=C/CC/C(=C/COC(=O)/C(=C/C(=O)O)/C)/C)/C)/C)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL470870
PubChem CID:   11154271
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 = 41.0 % PMID[487753]
NPT27 Others Unspecified Activity = 33.0 % PMID[487753]
NPT27 Others Unspecified Activity = 2.0 % PMID[487753]
NPT967 Individual Protein Xanthine dehydrogenase Homo sapiens Inhibition = 1.0 % PMID[487753]
NPT967 Individual Protein Xanthine dehydrogenase Homo sapiens Inhibition = 7.0 % PMID[487753]

☑ 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 NPC21946 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
0.9818 High Similarity NPC82465
0.9455 High Similarity NPC249850
0.9455 High Similarity NPC293437
0.9286 High Similarity NPC254095
0.9107 High Similarity NPC294938
0.9107 High Similarity NPC129150
0.9107 High Similarity NPC135863
0.8947 High Similarity NPC223679
0.8519 High Similarity NPC236338
0.8361 Intermediate Similarity NPC68110
0.8033 Intermediate Similarity NPC79756
0.7963 Intermediate Similarity NPC197467
0.7963 Intermediate Similarity NPC128280
0.7963 Intermediate Similarity NPC308331
0.7857 Intermediate Similarity NPC15789
0.7812 Intermediate Similarity NPC282760
0.7778 Intermediate Similarity NPC26600
0.7778 Intermediate Similarity NPC270706
0.7778 Intermediate Similarity NPC47946
0.7679 Intermediate Similarity NPC135698
0.7619 Intermediate Similarity NPC26810
0.7593 Intermediate Similarity NPC6963
0.7593 Intermediate Similarity NPC304079
0.7541 Intermediate Similarity NPC283502
0.7538 Intermediate Similarity NPC273600
0.75 Intermediate Similarity NPC473737
0.7424 Intermediate Similarity NPC146811
0.7414 Intermediate Similarity NPC43053
0.7391 Intermediate Similarity NPC316185
0.7353 Intermediate Similarity NPC151481
0.7344 Intermediate Similarity NPC55376
0.7344 Intermediate Similarity NPC151648
0.7333 Intermediate Similarity NPC478120
0.7313 Intermediate Similarity NPC203335
0.7302 Intermediate Similarity NPC97570
0.7273 Intermediate Similarity NPC12907
0.7246 Intermediate Similarity NPC59558
0.7231 Intermediate Similarity NPC179087
0.7231 Intermediate Similarity NPC44343
0.7231 Intermediate Similarity NPC210303
0.7231 Intermediate Similarity NPC2328
0.7222 Intermediate Similarity NPC203277
0.7188 Intermediate Similarity NPC130953
0.7188 Intermediate Similarity NPC98519
0.7183 Intermediate Similarity NPC315843
0.7164 Intermediate Similarity NPC475555
0.7164 Intermediate Similarity NPC475675
0.7164 Intermediate Similarity NPC248125
0.7143 Intermediate Similarity NPC293114
0.7143 Intermediate Similarity NPC474084
0.7143 Intermediate Similarity NPC189700
0.7097 Intermediate Similarity NPC96663
0.7059 Intermediate Similarity NPC122627
0.7049 Intermediate Similarity NPC218486
0.7049 Intermediate Similarity NPC474127
0.7042 Intermediate Similarity NPC284006
0.7031 Intermediate Similarity NPC286189
0.7027 Intermediate Similarity NPC279532
0.7015 Intermediate Similarity NPC471565
0.7015 Intermediate Similarity NPC470123
0.7015 Intermediate Similarity NPC471556
0.7015 Intermediate Similarity NPC19769
0.7015 Intermediate Similarity NPC471566
0.7015 Intermediate Similarity NPC96414
0.7 Intermediate Similarity NPC476037
0.7 Intermediate Similarity NPC469660
0.7 Intermediate Similarity NPC202011
0.6986 Remote Similarity NPC16279
0.6986 Remote Similarity NPC205615
0.6986 Remote Similarity NPC256640
0.6984 Remote Similarity NPC212730
0.6984 Remote Similarity NPC265551
0.6984 Remote Similarity NPC268185
0.697 Remote Similarity NPC155849
0.6944 Remote Similarity NPC107654
0.6944 Remote Similarity NPC114727
0.6944 Remote Similarity NPC476590
0.6935 Remote Similarity NPC478117
0.6923 Remote Similarity NPC471278
0.6923 Remote Similarity NPC161670
0.6923 Remote Similarity NPC474865
0.6923 Remote Similarity NPC26223
0.6912 Remote Similarity NPC201356
0.6909 Remote Similarity NPC57923
0.6909 Remote Similarity NPC41409
0.6901 Remote Similarity NPC84038
0.6892 Remote Similarity NPC51809
0.6892 Remote Similarity NPC176329
0.6892 Remote Similarity NPC474818
0.6892 Remote Similarity NPC125365
0.6892 Remote Similarity NPC49302
0.6885 Remote Similarity NPC477781
0.6885 Remote Similarity NPC477780
0.6875 Remote Similarity NPC471619
0.6866 Remote Similarity NPC470808
0.6857 Remote Similarity NPC475982
0.6857 Remote Similarity NPC88877
0.6857 Remote Similarity NPC476591
0.6852 Remote Similarity NPC12319
0.6852 Remote Similarity NPC18205
0.6849 Remote Similarity NPC478196
0.6849 Remote Similarity NPC478192
0.6849 Remote Similarity NPC478191
0.6849 Remote Similarity NPC478194
0.6849 Remote Similarity NPC478193
0.6849 Remote Similarity NPC478195
0.6849 Remote Similarity NPC260396
0.6842 Remote Similarity NPC160628
0.6825 Remote Similarity NPC51846
0.6825 Remote Similarity NPC245002
0.6825 Remote Similarity NPC221763
0.6825 Remote Similarity NPC150717
0.6812 Remote Similarity NPC132286
0.6812 Remote Similarity NPC225272
0.6812 Remote Similarity NPC478097
0.6812 Remote Similarity NPC194871
0.6806 Remote Similarity NPC474705
0.6806 Remote Similarity NPC329890
0.68 Remote Similarity NPC473471
0.68 Remote Similarity NPC279214
0.68 Remote Similarity NPC108816
0.68 Remote Similarity NPC221095
0.68 Remote Similarity NPC93763
0.6786 Remote Similarity NPC116934
0.678 Remote Similarity NPC267110
0.6774 Remote Similarity NPC159535
0.6774 Remote Similarity NPC151761
0.6769 Remote Similarity NPC302564
0.6765 Remote Similarity NPC478099
0.6765 Remote Similarity NPC478098
0.6761 Remote Similarity NPC4299
0.6761 Remote Similarity NPC67183
0.6761 Remote Similarity NPC476012
0.6761 Remote Similarity NPC473361
0.6761 Remote Similarity NPC329904
0.6757 Remote Similarity NPC301207
0.675 Remote Similarity NPC211892
0.6727 Remote Similarity NPC269823
0.6727 Remote Similarity NPC221250
0.6724 Remote Similarity NPC87137
0.6721 Remote Similarity NPC191643
0.6721 Remote Similarity NPC106531
0.6719 Remote Similarity NPC471279
0.6719 Remote Similarity NPC471277
0.6716 Remote Similarity NPC474658
0.6716 Remote Similarity NPC475073
0.6716 Remote Similarity NPC217940
0.6714 Remote Similarity NPC474823
0.6714 Remote Similarity NPC477117
0.6714 Remote Similarity NPC238223
0.6714 Remote Similarity NPC218477
0.6714 Remote Similarity NPC287705
0.6714 Remote Similarity NPC470256
0.6712 Remote Similarity NPC470686
0.6712 Remote Similarity NPC474758
0.6667 Remote Similarity NPC315115
0.6667 Remote Similarity NPC474913
0.6667 Remote Similarity NPC221467
0.6667 Remote Similarity NPC477087
0.6667 Remote Similarity NPC27264
0.6667 Remote Similarity NPC309408
0.6667 Remote Similarity NPC477086
0.6667 Remote Similarity NPC49028
0.6667 Remote Similarity NPC68156
0.6667 Remote Similarity NPC275530
0.6667 Remote Similarity NPC173157
0.6667 Remote Similarity NPC10572
0.6667 Remote Similarity NPC478101
0.6667 Remote Similarity NPC257618
0.6667 Remote Similarity NPC275316
0.6622 Remote Similarity NPC329852
0.662 Remote Similarity NPC475004
0.662 Remote Similarity NPC101622
0.6618 Remote Similarity NPC148233
0.6618 Remote Similarity NPC25747
0.6618 Remote Similarity NPC34883
0.6618 Remote Similarity NPC308457
0.6607 Remote Similarity NPC256766
0.6607 Remote Similarity NPC213538
0.6582 Remote Similarity NPC286770
0.6582 Remote Similarity NPC284472
0.6582 Remote Similarity NPC229799
0.6582 Remote Similarity NPC161045
0.6579 Remote Similarity NPC209135
0.6579 Remote Similarity NPC477314
0.6579 Remote Similarity NPC474816
0.6575 Remote Similarity NPC329914
0.6575 Remote Similarity NPC316851
0.6575 Remote Similarity NPC287878
0.6575 Remote Similarity NPC477085
0.6575 Remote Similarity NPC327383
0.6575 Remote Similarity NPC185186
0.6575 Remote Similarity NPC144419
0.6571 Remote Similarity NPC472266
0.6571 Remote Similarity NPC478100
0.6567 Remote Similarity NPC263732
0.6562 Remote Similarity NPC472808
0.6562 Remote Similarity NPC324224
0.6557 Remote Similarity NPC234829
0.6557 Remote Similarity NPC148056

  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 NPC21946 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
0.8036 Intermediate Similarity NPD6927 Phase 3
0.7368 Intermediate Similarity NPD4220 Pre-registration
0.6667 Remote Similarity NPD6096 Approved
0.6667 Remote Similarity NPD6097 Approved
0.661 Remote Similarity NPD5343 Approved
0.6552 Remote Similarity NPD4265 Approved
0.6522 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6491 Remote Similarity NPD9411 Phase 1
0.6393 Remote Similarity NPD2268 Discontinued
0.6377 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6271 Remote Similarity NPD39 Approved
0.6207 Remote Similarity NPD5326 Phase 3
0.6176 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6119 Remote Similarity NPD6109 Phase 1
0.6098 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6087 Remote Similarity NPD4191 Approved
0.6087 Remote Similarity NPD4194 Approved
0.6087 Remote Similarity NPD4192 Approved
0.6087 Remote Similarity NPD4193 Approved
0.6026 Remote Similarity NPD4756 Discovery
0.6 Remote Similarity NPD4222 Approved
0.6 Remote Similarity NPD9115 Approved
0.5974 Remote Similarity NPD1452 Discontinued
0.589 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5862 Remote Similarity NPD7838 Discovery
0.5857 Remote Similarity NPD9418 Clinical (unspecified phase)
0.5854 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5854 Remote Similarity NPD5209 Approved
0.5789 Remote Similarity NPD5783 Phase 3
0.5769 Remote Similarity NPD8039 Approved
0.5735 Remote Similarity NPD8779 Phase 3
0.5714 Remote Similarity NPD3173 Approved
0.5682 Remote Similarity NPD46 Approved
0.5682 Remote Similarity NPD5785 Approved
0.5682 Remote Similarity NPD6698 Approved
0.5652 Remote Similarity NPD585 Clinical (unspecified phase)
0.5647 Remote Similarity NPD6082 Clinical (unspecified phase)
0.561 Remote Similarity NPD5790 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