Structure

Physi-Chem Properties

Molecular Weight:  144.08
Volume:  138.886
LogP:  0.308
LogD:  0.836
LogS:  -0.058
# Rotatable Bonds:  0
TPSA:  52.99
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.451
Synthetic Accessibility Score:  4.274
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.814
MDCK Permeability:  8.255107968579978e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.345
Human Intestinal Absorption (HIA):  0.097
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.075

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.357
Plasma Protein Binding (PPB):  10.344695091247559%
Volume Distribution (VD):  0.969
Pgp-substrate:  79.16328430175781%

ADMET: Metabolism

CYP1A2-inhibitor:  0.16
CYP1A2-substrate:  0.504
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.788
CYP2C9-inhibitor:  0.003
CYP2C9-substrate:  0.135
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.251
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.13

ADMET: Excretion

Clearance (CL):  11.443
Half-life (T1/2):  0.813

ADMET: Toxicity

hERG Blockers:  0.04
Human Hepatotoxicity (H-HT):  0.439
Drug-inuced Liver Injury (DILI):  0.104
AMES Toxicity:  0.063
Rat Oral Acute Toxicity:  0.715
Maximum Recommended Daily Dose:  0.023
Skin Sensitization:  0.506
Carcinogencity:  0.65
Eye Corrosion:  0.985
Eye Irritation:  0.977
Respiratory Toxicity:  0.963

Download Data

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

  Natural Product: NPC476209

Natural Product ID:  NPC476209
Common Name*:   Ampelomin B
IUPAC Name:   (1S,2S,4S,5S,6R)-4-methyl-7-oxabicyclo[4.1.0]heptane-2,5-diol
Synonyms:   Ampelomin B
Standard InCHIKey:  CMZGQDPCPWKPGY-AZEWMMITSA-N
Standard InCHI:  InChI=1S/C7H12O3/c1-3-2-4(8)6-7(10-6)5(3)9/h3-9H,2H2,1H3/t3-,4-,5-,6-,7+/m0/s1
SMILES:  C[C@H]1C[C@H](O)[C@H]2[C@@H]([C@H]1O)O2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL553899
PubChem CID:   25243461
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001729] Oxepanes

*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
NPO32705 ampelomyces sp. Species Leptosphaeriaceae Eukaryota n.a. n.a. n.a. PMID[19193024]

☑ 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 IC50 > 10000000.0 nM PMID[456333]

☑ 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 NPC476209 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
0.9636 High Similarity NPC182903
0.8889 High Similarity NPC244869
0.8889 High Similarity NPC476136
0.8889 High Similarity NPC476149
0.8889 High Similarity NPC300235
0.7846 Intermediate Similarity NPC179823
0.7636 Intermediate Similarity NPC88638
0.7429 Intermediate Similarity NPC470151
0.7385 Intermediate Similarity NPC94897
0.7302 Intermediate Similarity NPC185116
0.7273 Intermediate Similarity NPC207656
0.7273 Intermediate Similarity NPC107091
0.7083 Intermediate Similarity NPC472950
0.7083 Intermediate Similarity NPC472952
0.7077 Intermediate Similarity NPC172622
0.7069 Intermediate Similarity NPC224987
0.7067 Intermediate Similarity NPC16449
0.7067 Intermediate Similarity NPC186588
0.7027 Intermediate Similarity NPC52755
0.6944 Remote Similarity NPC166250
0.6866 Remote Similarity NPC476702
0.6842 Remote Similarity NPC186594
0.6825 Remote Similarity NPC170780
0.6753 Remote Similarity NPC473257
0.6753 Remote Similarity NPC470156
0.675 Remote Similarity NPC475729
0.675 Remote Similarity NPC474215
0.6667 Remote Similarity NPC477447
0.6667 Remote Similarity NPC470155
0.6667 Remote Similarity NPC216800
0.6667 Remote Similarity NPC477446
0.6623 Remote Similarity NPC472943
0.6623 Remote Similarity NPC472951
0.6618 Remote Similarity NPC199937
0.6615 Remote Similarity NPC47663
0.6585 Remote Similarity NPC476379
0.6582 Remote Similarity NPC477978
0.6582 Remote Similarity NPC227170
0.6582 Remote Similarity NPC241959
0.6579 Remote Similarity NPC272841
0.6579 Remote Similarity NPC43463
0.6545 Remote Similarity NPC88278
0.6545 Remote Similarity NPC111882
0.6545 Remote Similarity NPC227707
0.6545 Remote Similarity NPC99573
0.6545 Remote Similarity NPC102981
0.6538 Remote Similarity NPC211049
0.6538 Remote Similarity NPC470154
0.6533 Remote Similarity NPC136424
0.6528 Remote Similarity NPC471879
0.6486 Remote Similarity NPC308489
0.6462 Remote Similarity NPC322148
0.642 Remote Similarity NPC298595
0.6418 Remote Similarity NPC475412
0.6406 Remote Similarity NPC471269
0.6389 Remote Similarity NPC470833
0.6379 Remote Similarity NPC240994
0.6364 Remote Similarity NPC191345
0.6364 Remote Similarity NPC252483
0.6364 Remote Similarity NPC147993
0.6364 Remote Similarity NPC471769
0.6341 Remote Similarity NPC235196
0.6341 Remote Similarity NPC228593
0.6341 Remote Similarity NPC268633
0.6338 Remote Similarity NPC57788
0.6338 Remote Similarity NPC53879
0.6329 Remote Similarity NPC116320
0.6329 Remote Similarity NPC119922
0.6324 Remote Similarity NPC475807
0.6296 Remote Similarity NPC320824
0.629 Remote Similarity NPC307022
0.6282 Remote Similarity NPC477282
0.6282 Remote Similarity NPC81074
0.6269 Remote Similarity NPC174485
0.6267 Remote Similarity NPC192501
0.6267 Remote Similarity NPC228994
0.6267 Remote Similarity NPC10476
0.6265 Remote Similarity NPC110365
0.6265 Remote Similarity NPC213658
0.6265 Remote Similarity NPC45833
0.6265 Remote Similarity NPC62202
0.625 Remote Similarity NPC266553
0.6234 Remote Similarity NPC476719
0.6234 Remote Similarity NPC476233
0.6203 Remote Similarity NPC117137
0.6203 Remote Similarity NPC66766
0.6184 Remote Similarity NPC196136
0.6184 Remote Similarity NPC158208
0.6184 Remote Similarity NPC243027
0.6167 Remote Similarity NPC223468
0.6167 Remote Similarity NPC147343
0.6167 Remote Similarity NPC287550
0.6167 Remote Similarity NPC198540
0.6167 Remote Similarity NPC84030
0.6167 Remote Similarity NPC176309
0.6163 Remote Similarity NPC114389
0.6154 Remote Similarity NPC177343
0.6154 Remote Similarity NPC13823
0.6154 Remote Similarity NPC68119
0.6145 Remote Similarity NPC107603
0.6145 Remote Similarity NPC471240
0.6136 Remote Similarity NPC469583
0.6119 Remote Similarity NPC87296
0.6119 Remote Similarity NPC475515
0.6119 Remote Similarity NPC215671
0.6111 Remote Similarity NPC477758
0.6111 Remote Similarity NPC477760
0.6111 Remote Similarity NPC477761
0.6111 Remote Similarity NPC477759
0.6111 Remote Similarity NPC477754
0.6104 Remote Similarity NPC470145
0.6092 Remote Similarity NPC475307
0.6092 Remote Similarity NPC119379
0.6076 Remote Similarity NPC269333
0.6071 Remote Similarity NPC471377
0.6071 Remote Similarity NPC5943
0.6067 Remote Similarity NPC472996
0.6067 Remote Similarity NPC472997
0.6066 Remote Similarity NPC14144
0.6056 Remote Similarity NPC165069
0.6053 Remote Similarity NPC475458
0.6049 Remote Similarity NPC475388
0.6049 Remote Similarity NPC60018
0.6049 Remote Similarity NPC202688
0.6049 Remote Similarity NPC154043
0.6032 Remote Similarity NPC474331
0.6026 Remote Similarity NPC474574
0.6026 Remote Similarity NPC133596
0.6026 Remote Similarity NPC128951
0.6026 Remote Similarity NPC192046
0.6026 Remote Similarity NPC64081
0.6026 Remote Similarity NPC477227
0.6026 Remote Similarity NPC105208
0.6026 Remote Similarity NPC11907
0.6026 Remote Similarity NPC302578
0.6024 Remote Similarity NPC266651
0.6024 Remote Similarity NPC478111
0.6 Remote Similarity NPC474994
0.6 Remote Similarity NPC95124
0.6 Remote Similarity NPC476040
0.6 Remote Similarity NPC8004
0.6 Remote Similarity NPC471266
0.6 Remote Similarity NPC472998
0.6 Remote Similarity NPC127283
0.6 Remote Similarity NPC476021
0.6 Remote Similarity NPC470872
0.6 Remote Similarity NPC473436
0.5977 Remote Similarity NPC91251
0.5976 Remote Similarity NPC69953
0.5974 Remote Similarity NPC231680
0.5974 Remote Similarity NPC91387
0.5974 Remote Similarity NPC270306
0.5974 Remote Similarity NPC244539
0.5972 Remote Similarity NPC477756
0.5972 Remote Similarity NPC477751
0.5972 Remote Similarity NPC477752
0.5972 Remote Similarity NPC477764
0.5968 Remote Similarity NPC157193
0.5968 Remote Similarity NPC42503
0.5968 Remote Similarity NPC282143
0.5968 Remote Similarity NPC299781
0.5955 Remote Similarity NPC17336
0.5952 Remote Similarity NPC215968
0.5952 Remote Similarity NPC255143
0.5952 Remote Similarity NPC471411
0.5952 Remote Similarity NPC155531
0.5952 Remote Similarity NPC279260
0.5952 Remote Similarity NPC246347
0.5952 Remote Similarity NPC472379
0.5952 Remote Similarity NPC471410
0.5952 Remote Similarity NPC131365
0.5949 Remote Similarity NPC67657
0.5949 Remote Similarity NPC477089
0.5949 Remote Similarity NPC18857
0.5949 Remote Similarity NPC475725
0.5932 Remote Similarity NPC320240
0.5932 Remote Similarity NPC70756
0.5932 Remote Similarity NPC144891
0.593 Remote Similarity NPC161560
0.5926 Remote Similarity NPC471270
0.5921 Remote Similarity NPC470660
0.5921 Remote Similarity NPC95165
0.5921 Remote Similarity NPC470659
0.5921 Remote Similarity NPC476709
0.5909 Remote Similarity NPC137461
0.5904 Remote Similarity NPC86238
0.5904 Remote Similarity NPC474156
0.5904 Remote Similarity NPC18953
0.5902 Remote Similarity NPC314613
0.5902 Remote Similarity NPC230789
0.5902 Remote Similarity NPC252918
0.5902 Remote Similarity NPC277475
0.5902 Remote Similarity NPC8597
0.5902 Remote Similarity NPC321087
0.5897 Remote Similarity NPC163597
0.5897 Remote Similarity NPC313762
0.5897 Remote Similarity NPC293223
0.5897 Remote Similarity NPC107963
0.589 Remote Similarity NPC476650
0.5889 Remote Similarity NPC477264

  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 NPC476209 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
0.7937 Intermediate Similarity NPD371 Approved
0.7761 Intermediate Similarity NPD7532 Clinical (unspecified phase)
0.7273 Intermediate Similarity NPD9218 Clinical (unspecified phase)
0.7273 Intermediate Similarity NPD9219 Approved
0.6545 Remote Similarity NPD8996 Phase 3
0.6545 Remote Similarity NPD8995 Clinical (unspecified phase)
0.6316 Remote Similarity NPD8958 Phase 2
0.6167 Remote Similarity NPD384 Approved
0.6167 Remote Similarity NPD385 Approved
0.5862 Remote Similarity NPD3168 Discontinued
0.5844 Remote Similarity NPD1810 Approved
0.5844 Remote Similarity NPD1811 Approved
0.5806 Remote Similarity NPD5344 Discontinued
0.5763 Remote Similarity NPD8957 Approved
0.5738 Remote Similarity NPD8994 Approved
0.5738 Remote Similarity NPD386 Approved
0.5738 Remote Similarity NPD8997 Approved
0.5738 Remote Similarity NPD388 Approved
0.5738 Remote Similarity NPD8998 Phase 2
0.5738 Remote Similarity NPD8999 Phase 3
0.5738 Remote Similarity NPD8993 Phase 1
0.5738 Remote Similarity NPD9000 Phase 3
0.5714 Remote Similarity NPD9061 Clinical (unspecified phase)
0.5667 Remote Similarity NPD9006 Approved
0.5636 Remote Similarity NPD9052 Approved
0.5636 Remote Similarity NPD9053 Approved
0.5636 Remote Similarity NPD9051 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