Structure

Physi-Chem Properties

Molecular Weight:  294.11
Volume:  296.362
LogP:  0.472
LogD:  0.329
LogS:  -1.229
# Rotatable Bonds:  7
TPSA:  93.81
# H-Bond Aceptor:  6
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.629
Synthetic Accessibility Score:  3.619
Fsp3:  0.4
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.671
MDCK Permeability:  2.1384570572990924e-05
Pgp-inhibitor:  0.01
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.017
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.165

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.385
Plasma Protein Binding (PPB):  85.2743911743164%
Volume Distribution (VD):  0.306
Pgp-substrate:  20.2728328704834%

ADMET: Metabolism

CYP1A2-inhibitor:  0.43
CYP1A2-substrate:  0.751
CYP2C19-inhibitor:  0.435
CYP2C19-substrate:  0.089
CYP2C9-inhibitor:  0.351
CYP2C9-substrate:  0.713
CYP2D6-inhibitor:  0.127
CYP2D6-substrate:  0.434
CYP3A4-inhibitor:  0.036
CYP3A4-substrate:  0.249

ADMET: Excretion

Clearance (CL):  7.065
Half-life (T1/2):  0.919

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.346
Drug-inuced Liver Injury (DILI):  0.575
AMES Toxicity:  0.122
Rat Oral Acute Toxicity:  0.071
Maximum Recommended Daily Dose:  0.156
Skin Sensitization:  0.415
Carcinogencity:  0.53
Eye Corrosion:  0.004
Eye Irritation:  0.072
Respiratory Toxicity:  0.107

Download Data

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

  Natural Product: NPC475675

Natural Product ID:  NPC475675
Common Name*:   6,7-(E)-Phomopsolide A
IUPAC Name:   [(2S,3S)-2-[(E)-4-hydroxy-3-oxopent-1-enyl]-6-oxo-2,3-dihydropyran-3-yl] (E)-2-methylbut-2-enoate
Synonyms:   6,7-(E)-Phomopsolide A
Standard InCHIKey:  LJWPJGJLPBFTPH-BQQCSXKUSA-N
Standard InCHI:  InChI=1S/C15H18O6/c1-4-9(2)15(19)21-13-7-8-14(18)20-12(13)6-5-11(17)10(3)16/h4-8,10,12-13,16H,1-3H3/b6-5+,9-4+/t10?,12-,13-/m0/s1
SMILES:  C/C=C(/C(=O)O[C@H]1C=CC(=O)O[C@H]1/C=C/C(=O)C(O)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL511194
PubChem CID:   44559465
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000086] Pyrans
        • [CHEMONTID:0000481] Pyranones and derivatives
          • [CHEMONTID:0001211] Dihydropyranones

*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
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[10479323]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[12350167]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[14640527]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota Axinella verrucosa Mediterranean n.a. PMID[14738391]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15043411]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. Sussex Inlet, New South Wales, Australia n.a. PMID[15104517]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15332862]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. Berkeley Pit lake n.a. PMID[17970594]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. New Zealand n.a. PMID[19323568]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19326880]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[20452770]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. North Sea n.a. PMID[21126094]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21126094]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. Limonium tubiflorum n.a. PMID[21146414]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21916432]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22148349]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22458669]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23360521]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23477451]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23603293]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23972215]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24033077]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24437979]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[31433188]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[9392888]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[Article]

☑ 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 22.0 mm PMID[459455]

☑ 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 NPC475675 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
1.0 High Similarity NPC475555
0.9206 High Similarity NPC273600
0.8413 Intermediate Similarity NPC302564
0.8333 Intermediate Similarity NPC96414
0.8209 Intermediate Similarity NPC201356
0.8088 Intermediate Similarity NPC122627
0.8 Intermediate Similarity NPC202011
0.7857 Intermediate Similarity NPC475982
0.7838 Intermediate Similarity NPC475711
0.7821 Intermediate Similarity NPC474251
0.7812 Intermediate Similarity NPC135863
0.7794 Intermediate Similarity NPC19769
0.7746 Intermediate Similarity NPC59558
0.7727 Intermediate Similarity NPC26223
0.7703 Intermediate Similarity NPC203277
0.7692 Intermediate Similarity NPC254095
0.7692 Intermediate Similarity NPC223679
0.7541 Intermediate Similarity NPC15789
0.7541 Intermediate Similarity NPC275316
0.7538 Intermediate Similarity NPC249850
0.7538 Intermediate Similarity NPC129150
0.7538 Intermediate Similarity NPC293437
0.75 Intermediate Similarity NPC2328
0.75 Intermediate Similarity NPC473737
0.75 Intermediate Similarity NPC279532
0.7467 Intermediate Similarity NPC470705
0.7432 Intermediate Similarity NPC107654
0.7429 Intermediate Similarity NPC276299
0.7391 Intermediate Similarity NPC25747
0.7391 Intermediate Similarity NPC470808
0.7391 Intermediate Similarity NPC308457
0.7391 Intermediate Similarity NPC148233
0.7385 Intermediate Similarity NPC230296
0.7385 Intermediate Similarity NPC150717
0.7385 Intermediate Similarity NPC221763
0.7361 Intermediate Similarity NPC151481
0.7353 Intermediate Similarity NPC26810
0.7313 Intermediate Similarity NPC82465
0.7313 Intermediate Similarity NPC97570
0.7286 Intermediate Similarity NPC470123
0.7286 Intermediate Similarity NPC282760
0.7273 Intermediate Similarity NPC28049
0.7273 Intermediate Similarity NPC318481
0.7273 Intermediate Similarity NPC294938
0.7258 Intermediate Similarity NPC236338
0.725 Intermediate Similarity NPC44261
0.7246 Intermediate Similarity NPC474774
0.7222 Intermediate Similarity NPC238223
0.7222 Intermediate Similarity NPC474823
0.7206 Intermediate Similarity NPC98519
0.7206 Intermediate Similarity NPC130953
0.7206 Intermediate Similarity NPC79756
0.72 Intermediate Similarity NPC315843
0.72 Intermediate Similarity NPC114727
0.72 Intermediate Similarity NPC476590
0.7188 Intermediate Similarity NPC477781
0.7188 Intermediate Similarity NPC477780
0.7183 Intermediate Similarity NPC146811
0.7183 Intermediate Similarity NPC478101
0.7183 Intermediate Similarity NPC124586
0.7164 Intermediate Similarity NPC21946
0.7162 Intermediate Similarity NPC316185
0.7143 Intermediate Similarity NPC474026
0.7123 Intermediate Similarity NPC475004
0.7121 Intermediate Similarity NPC51846
0.7105 Intermediate Similarity NPC478196
0.7105 Intermediate Similarity NPC478191
0.7105 Intermediate Similarity NPC161038
0.7105 Intermediate Similarity NPC478193
0.7105 Intermediate Similarity NPC478194
0.7105 Intermediate Similarity NPC478195
0.7105 Intermediate Similarity NPC478192
0.7101 Intermediate Similarity NPC55376
0.7101 Intermediate Similarity NPC151648
0.7089 Intermediate Similarity NPC121374
0.7083 Intermediate Similarity NPC478100
0.7083 Intermediate Similarity NPC203335
0.7083 Intermediate Similarity NPC132286
0.7067 Intermediate Similarity NPC327383
0.7067 Intermediate Similarity NPC185186
0.7067 Intermediate Similarity NPC316851
0.7059 Intermediate Similarity NPC159650
0.7059 Intermediate Similarity NPC22897
0.7051 Intermediate Similarity NPC473471
0.7051 Intermediate Similarity NPC248775
0.7042 Intermediate Similarity NPC478099
0.7042 Intermediate Similarity NPC471566
0.7042 Intermediate Similarity NPC478098
0.7042 Intermediate Similarity NPC7940
0.7042 Intermediate Similarity NPC471565
0.7042 Intermediate Similarity NPC476589
0.7037 Intermediate Similarity NPC161045
0.7037 Intermediate Similarity NPC16488
0.7015 Intermediate Similarity NPC71755
0.7013 Intermediate Similarity NPC209113
0.7013 Intermediate Similarity NPC256640
0.7013 Intermediate Similarity NPC205615
0.7013 Intermediate Similarity NPC127118
0.7013 Intermediate Similarity NPC16279
0.7013 Intermediate Similarity NPC301207
0.7 Intermediate Similarity NPC112868
0.7 Intermediate Similarity NPC475073
0.7 Intermediate Similarity NPC179087
0.7 Intermediate Similarity NPC210303
0.7 Intermediate Similarity NPC297440
0.7 Intermediate Similarity NPC44343
0.7 Intermediate Similarity NPC68110
0.6986 Remote Similarity NPC63873
0.6986 Remote Similarity NPC475760
0.6974 Remote Similarity NPC473489
0.6962 Remote Similarity NPC99651
0.6962 Remote Similarity NPC470148
0.6962 Remote Similarity NPC470149
0.6962 Remote Similarity NPC180725
0.6957 Remote Similarity NPC309408
0.6944 Remote Similarity NPC37382
0.6933 Remote Similarity NPC293114
0.6923 Remote Similarity NPC176329
0.6923 Remote Similarity NPC51809
0.6923 Remote Similarity NPC275530
0.6923 Remote Similarity NPC49302
0.6923 Remote Similarity NPC116366
0.6923 Remote Similarity NPC125365
0.6923 Remote Similarity NPC327103
0.6923 Remote Similarity NPC474818
0.6912 Remote Similarity NPC187770
0.6912 Remote Similarity NPC189700
0.6892 Remote Similarity NPC130618
0.6883 Remote Similarity NPC260396
0.6883 Remote Similarity NPC315552
0.6883 Remote Similarity NPC285840
0.6883 Remote Similarity NPC327041
0.6883 Remote Similarity NPC473582
0.6875 Remote Similarity NPC470147
0.6875 Remote Similarity NPC133226
0.6867 Remote Similarity NPC67081
0.6867 Remote Similarity NPC470124
0.6867 Remote Similarity NPC11804
0.6867 Remote Similarity NPC471223
0.686 Remote Similarity NPC274075
0.6857 Remote Similarity NPC263732
0.6849 Remote Similarity NPC478097
0.6842 Remote Similarity NPC284006
0.6835 Remote Similarity NPC279214
0.6835 Remote Similarity NPC477314
0.6835 Remote Similarity NPC221095
0.6829 Remote Similarity NPC315559
0.6818 Remote Similarity NPC478120
0.6818 Remote Similarity NPC218486
0.6818 Remote Similarity NPC135537
0.6812 Remote Similarity NPC286189
0.6806 Remote Similarity NPC182794
0.6806 Remote Similarity NPC471556
0.68 Remote Similarity NPC329904
0.68 Remote Similarity NPC476037
0.68 Remote Similarity NPC473361
0.68 Remote Similarity NPC476012
0.6786 Remote Similarity NPC315395
0.6786 Remote Similarity NPC316426
0.6782 Remote Similarity NPC32552
0.6769 Remote Similarity NPC191643
0.6765 Remote Similarity NPC283502
0.6765 Remote Similarity NPC319423
0.6757 Remote Similarity NPC477117
0.6757 Remote Similarity NPC310210
0.6753 Remote Similarity NPC326504
0.675 Remote Similarity NPC139712
0.6747 Remote Similarity NPC161670
0.6747 Remote Similarity NPC475035
0.6716 Remote Similarity NPC173157
0.6712 Remote Similarity NPC248125
0.6712 Remote Similarity NPC470033
0.6711 Remote Similarity NPC178575
0.6711 Remote Similarity NPC475762
0.6709 Remote Similarity NPC315394
0.6709 Remote Similarity NPC471225
0.6709 Remote Similarity NPC474278
0.6707 Remote Similarity NPC313677
0.6707 Remote Similarity NPC310450
0.6707 Remote Similarity NPC475046
0.6707 Remote Similarity NPC474959
0.6707 Remote Similarity NPC11383
0.6706 Remote Similarity NPC45409
0.6667 Remote Similarity NPC182383
0.6667 Remote Similarity NPC473948
0.6667 Remote Similarity NPC475618
0.6667 Remote Similarity NPC88877
0.6667 Remote Similarity NPC474084
0.6667 Remote Similarity NPC475034
0.6667 Remote Similarity NPC476591
0.6627 Remote Similarity NPC284472
0.6627 Remote Similarity NPC253801
0.6627 Remote Similarity NPC229799
0.6627 Remote Similarity NPC286770
0.6627 Remote Similarity NPC144415
0.6625 Remote Similarity NPC182292
0.6623 Remote Similarity NPC329890
0.6623 Remote Similarity NPC329914
0.6622 Remote Similarity NPC25298
0.6622 Remote Similarity NPC225272

  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 NPC475675 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
0.6912 Remote Similarity NPD9119 Approved
0.6912 Remote Similarity NPD69 Approved
0.6765 Remote Similarity NPD9118 Approved
0.6667 Remote Similarity NPD6109 Phase 1
0.6429 Remote Similarity NPD585 Clinical (unspecified phase)
0.6364 Remote Similarity NPD6927 Phase 3
0.6349 Remote Similarity NPD9090 Phase 3
0.6296 Remote Similarity NPD4756 Discovery
0.6292 Remote Similarity NPD7838 Discovery
0.6163 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6111 Remote Similarity NPD46 Approved
0.6111 Remote Similarity NPD6698 Approved
0.6061 Remote Similarity NPD4220 Pre-registration
0.6 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5921 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5873 Remote Similarity NPD9297 Discontinued
0.5873 Remote Similarity NPD9091 Suspended
0.5862 Remote Similarity NPD6110 Phase 1
0.5833 Remote Similarity NPD8779 Phase 3
0.5833 Remote Similarity NPD4225 Approved
0.5811 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5789 Remote Similarity NPD3197 Phase 1
0.5781 Remote Similarity NPD9411 Phase 1
0.5769 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5761 Remote Similarity NPD5785 Approved
0.5747 Remote Similarity NPD5209 Approved
0.5733 Remote Similarity NPD9418 Clinical (unspecified phase)
0.5714 Remote Similarity NPD5344 Discontinued
0.5692 Remote Similarity NPD6096 Approved
0.5692 Remote Similarity NPD6097 Approved
0.5684 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5663 Remote Similarity NPD1452 Discontinued
0.5658 Remote Similarity NPD2664 Clinical (unspecified phase)
0.5641 Remote Similarity NPD3704 Approved
0.5625 Remote Similarity NPD4792 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