Structure

Physi-Chem Properties

Molecular Weight:  184.07
Volume:  182.915
LogP:  2.104
LogD:  1.519
LogS:  -1.884
# Rotatable Bonds:  3
TPSA:  70.67
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.753
Synthetic Accessibility Score:  2.928
Fsp3:  0.444
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:  -5.239
MDCK Permeability:  1.4711788935528602e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.008
Human Intestinal Absorption (HIA):  0.015
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.04

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.101
Plasma Protein Binding (PPB):  93.62609100341797%
Volume Distribution (VD):  0.455
Pgp-substrate:  8.861526489257812%

ADMET: Metabolism

CYP1A2-inhibitor:  0.06
CYP1A2-substrate:  0.318
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.056
CYP2C9-inhibitor:  0.054
CYP2C9-substrate:  0.151
CYP2D6-inhibitor:  0.02
CYP2D6-substrate:  0.121
CYP3A4-inhibitor:  0.02
CYP3A4-substrate:  0.053

ADMET: Excretion

Clearance (CL):  3.369
Half-life (T1/2):  0.885

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.788
Drug-inuced Liver Injury (DILI):  0.982
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.77
Maximum Recommended Daily Dose:  0.009
Skin Sensitization:  0.452
Carcinogencity:  0.476
Eye Corrosion:  0.068
Eye Irritation:  0.689
Respiratory Toxicity:  0.734

Download Data

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

  Natural Product: NPC48641

Natural Product ID:  NPC48641
Common Name*:   (2R,3S)-4-Methylidene-5-Oxo-2-Propyloxolane-3-Carboxylic Acid
IUPAC Name:   (2R,3S)-4-methylidene-5-oxo-2-propyloxolane-3-carboxylic acid
Synonyms:  
Standard InCHIKey:  SRQUTZJZABSZRQ-RQJHMYQMSA-N
Standard InCHI:  InChI=1S/C9H12O4/c1-3-4-6-7(8(10)11)5(2)9(12)13-6/h6-7H,2-4H2,1H3,(H,10,11)/t6-,7+/m1/s1
SMILES:  CCC[C@H]1OC(=O)C(=C)[C@@H]1C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL217676
PubChem CID:   21579153
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001245] Gamma butyrolactones

*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
NPO16865.1 Prunus serrulata var. spontanea Varieties Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16865.1 Prunus serrulata var. spontanea Varieties Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16885 Phonus arborescens Species Asteraceae 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
NPT466 Cell Line U-937 Homo sapiens Activity = 44.0 % PMID[496359]
NPT1079 Individual Protein Histone acetyltransferase p300 Homo sapiens Activity = 58.6 % PMID[496361]
NPT1834 Individual Protein CREB-binding protein Homo sapiens Activity = 45.9 % PMID[496361]
NPT443 Individual Protein Histone acetyltransferase GCN5 Homo sapiens Activity = 54.5 % PMID[496361]
NPT1080 Individual Protein Histone acetyltransferase PCAF Homo sapiens Activity = 76.8 % PMID[496361]
NPT443 Individual Protein Histone acetyltransferase GCN5 Homo sapiens IC50 = 100000.0 nM PMID[496362]
NPT443 Individual Protein Histone acetyltransferase GCN5 Homo sapiens IC50 = 100000.0 nM PMID[496363]
NPT2 Others Unspecified Activity = 55.0 % PMID[496360]
NPT2 Others Unspecified Inhibition = 44.0 % PMID[496361]

☑ 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 NPC48641 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
0.9315 High Similarity NPC19841
0.8481 Intermediate Similarity NPC158756
0.8375 Intermediate Similarity NPC470755
0.8333 Intermediate Similarity NPC24417
0.8312 Intermediate Similarity NPC167881
0.8312 Intermediate Similarity NPC98557
0.8272 Intermediate Similarity NPC469910
0.8228 Intermediate Similarity NPC229825
0.8182 Intermediate Similarity NPC108816
0.8182 Intermediate Similarity NPC93763
0.8125 Intermediate Similarity NPC40746
0.8125 Intermediate Similarity NPC169575
0.8125 Intermediate Similarity NPC59097
0.8125 Intermediate Similarity NPC131669
0.8125 Intermediate Similarity NPC473390
0.8072 Intermediate Similarity NPC476803
0.8072 Intermediate Similarity NPC475819
0.8072 Intermediate Similarity NPC476805
0.8052 Intermediate Similarity NPC141789
0.8052 Intermediate Similarity NPC7563
0.8052 Intermediate Similarity NPC320630
0.8052 Intermediate Similarity NPC116177
0.8052 Intermediate Similarity NPC476028
0.8052 Intermediate Similarity NPC171204
0.8052 Intermediate Similarity NPC97516
0.8025 Intermediate Similarity NPC114979
0.8025 Intermediate Similarity NPC96259
0.8025 Intermediate Similarity NPC141193
0.8025 Intermediate Similarity NPC191476
0.8025 Intermediate Similarity NPC476804
0.7976 Intermediate Similarity NPC12872
0.7976 Intermediate Similarity NPC168679
0.7971 Intermediate Similarity NPC472328
0.7952 Intermediate Similarity NPC201658
0.7949 Intermediate Similarity NPC471465
0.7949 Intermediate Similarity NPC267231
0.7949 Intermediate Similarity NPC196653
0.7927 Intermediate Similarity NPC255307
0.7927 Intermediate Similarity NPC165162
0.7895 Intermediate Similarity NPC476355
0.7895 Intermediate Similarity NPC140287
0.7882 Intermediate Similarity NPC19087
0.7882 Intermediate Similarity NPC474232
0.7875 Intermediate Similarity NPC52861
0.7867 Intermediate Similarity NPC474590
0.7867 Intermediate Similarity NPC163003
0.7848 Intermediate Similarity NPC470239
0.7848 Intermediate Similarity NPC270126
0.7848 Intermediate Similarity NPC470244
0.7831 Intermediate Similarity NPC475461
0.7831 Intermediate Similarity NPC469483
0.7831 Intermediate Similarity NPC150755
0.7831 Intermediate Similarity NPC236692
0.7831 Intermediate Similarity NPC305475
0.7831 Intermediate Similarity NPC309757
0.7831 Intermediate Similarity NPC162071
0.7791 Intermediate Similarity NPC184063
0.7778 Intermediate Similarity NPC89555
0.7765 Intermediate Similarity NPC38392
0.7763 Intermediate Similarity NPC58956
0.7763 Intermediate Similarity NPC269206
0.7763 Intermediate Similarity NPC295633
0.775 Intermediate Similarity NPC281132
0.775 Intermediate Similarity NPC223904
0.7701 Intermediate Similarity NPC469692
0.7701 Intermediate Similarity NPC469645
0.7701 Intermediate Similarity NPC475302
0.7692 Intermediate Similarity NPC68819
0.7692 Intermediate Similarity NPC123360
0.7683 Intermediate Similarity NPC245665
0.7654 Intermediate Similarity NPC281949
0.7654 Intermediate Similarity NPC301477
0.7654 Intermediate Similarity NPC25684
0.7654 Intermediate Similarity NPC141810
0.7647 Intermediate Similarity NPC207114
0.7647 Intermediate Similarity NPC477302
0.7647 Intermediate Similarity NPC136879
0.7647 Intermediate Similarity NPC217983
0.7647 Intermediate Similarity NPC473715
0.7647 Intermediate Similarity NPC79549
0.7639 Intermediate Similarity NPC470325
0.7639 Intermediate Similarity NPC53642
0.7625 Intermediate Similarity NPC617
0.7625 Intermediate Similarity NPC178277
0.7619 Intermediate Similarity NPC470242
0.7619 Intermediate Similarity NPC187661
0.7619 Intermediate Similarity NPC261721
0.7619 Intermediate Similarity NPC238593
0.7619 Intermediate Similarity NPC304558
0.7614 Intermediate Similarity NPC121825
0.7595 Intermediate Similarity NPC476794
0.7595 Intermediate Similarity NPC474760
0.7595 Intermediate Similarity NPC470240
0.7595 Intermediate Similarity NPC122847
0.759 Intermediate Similarity NPC156485
0.7586 Intermediate Similarity NPC261607
0.7586 Intermediate Similarity NPC111114
0.7586 Intermediate Similarity NPC300312
0.7564 Intermediate Similarity NPC193351
0.7564 Intermediate Similarity NPC138408
0.7564 Intermediate Similarity NPC155587
0.7564 Intermediate Similarity NPC226669
0.7558 Intermediate Similarity NPC206001
0.7558 Intermediate Similarity NPC155935
0.7558 Intermediate Similarity NPC215556
0.7558 Intermediate Similarity NPC218927
0.7531 Intermediate Similarity NPC6823
0.7529 Intermediate Similarity NPC266957
0.7529 Intermediate Similarity NPC118601
0.7529 Intermediate Similarity NPC186148
0.7529 Intermediate Similarity NPC190753
0.7528 Intermediate Similarity NPC193645
0.7528 Intermediate Similarity NPC471142
0.7528 Intermediate Similarity NPC90121
0.7528 Intermediate Similarity NPC475659
0.7528 Intermediate Similarity NPC477922
0.7528 Intermediate Similarity NPC275960
0.7528 Intermediate Similarity NPC475900
0.7528 Intermediate Similarity NPC48803
0.75 Intermediate Similarity NPC21469
0.75 Intermediate Similarity NPC473263
0.75 Intermediate Similarity NPC153590
0.75 Intermediate Similarity NPC473273
0.75 Intermediate Similarity NPC60386
0.75 Intermediate Similarity NPC308656
0.75 Intermediate Similarity NPC473234
0.7471 Intermediate Similarity NPC297474
0.7471 Intermediate Similarity NPC206614
0.7471 Intermediate Similarity NPC71533
0.7471 Intermediate Similarity NPC106510
0.7471 Intermediate Similarity NPC473619
0.7471 Intermediate Similarity NPC144133
0.7471 Intermediate Similarity NPC129419
0.7471 Intermediate Similarity NPC469368
0.7471 Intermediate Similarity NPC474323
0.7471 Intermediate Similarity NPC35809
0.7471 Intermediate Similarity NPC179394
0.7471 Intermediate Similarity NPC216284
0.7471 Intermediate Similarity NPC475855
0.7471 Intermediate Similarity NPC54065
0.747 Intermediate Similarity NPC318468
0.747 Intermediate Similarity NPC475947
0.747 Intermediate Similarity NPC128429
0.747 Intermediate Similarity NPC116543
0.747 Intermediate Similarity NPC250315
0.7468 Intermediate Similarity NPC235906
0.7444 Intermediate Similarity NPC158416
0.7444 Intermediate Similarity NPC91771
0.7444 Intermediate Similarity NPC230800
0.7444 Intermediate Similarity NPC76862
0.7444 Intermediate Similarity NPC477921
0.7444 Intermediate Similarity NPC39859
0.7444 Intermediate Similarity NPC142529
0.7444 Intermediate Similarity NPC476009
0.7444 Intermediate Similarity NPC473859
0.7444 Intermediate Similarity NPC470883
0.7442 Intermediate Similarity NPC58219
0.7442 Intermediate Similarity NPC177629
0.7442 Intermediate Similarity NPC202672
0.7442 Intermediate Similarity NPC178875
0.7439 Intermediate Similarity NPC471325
0.7436 Intermediate Similarity NPC114727
0.7436 Intermediate Similarity NPC476590
0.7436 Intermediate Similarity NPC320537
0.7436 Intermediate Similarity NPC143979
0.7416 Intermediate Similarity NPC473331
0.7416 Intermediate Similarity NPC167219
0.7412 Intermediate Similarity NPC9231
0.7412 Intermediate Similarity NPC85698
0.7386 Intermediate Similarity NPC35959
0.7386 Intermediate Similarity NPC473321
0.7386 Intermediate Similarity NPC57304
0.7386 Intermediate Similarity NPC171360
0.7386 Intermediate Similarity NPC293001
0.7386 Intermediate Similarity NPC63193
0.7386 Intermediate Similarity NPC184463
0.7386 Intermediate Similarity NPC475881
0.7386 Intermediate Similarity NPC155215
0.7386 Intermediate Similarity NPC70251
0.7386 Intermediate Similarity NPC131209
0.7386 Intermediate Similarity NPC133888
0.7386 Intermediate Similarity NPC29821
0.7386 Intermediate Similarity NPC133698
0.7381 Intermediate Similarity NPC138647
0.7381 Intermediate Similarity NPC194859
0.7381 Intermediate Similarity NPC224386
0.7381 Intermediate Similarity NPC470238
0.7381 Intermediate Similarity NPC159635
0.7381 Intermediate Similarity NPC115786
0.7375 Intermediate Similarity NPC65603
0.7375 Intermediate Similarity NPC41780
0.7375 Intermediate Similarity NPC187568
0.7375 Intermediate Similarity NPC57744
0.7363 Intermediate Similarity NPC169205
0.7363 Intermediate Similarity NPC471462
0.7363 Intermediate Similarity NPC311904
0.7363 Intermediate Similarity NPC474313
0.7356 Intermediate Similarity NPC307411
0.7356 Intermediate Similarity NPC92974
0.7356 Intermediate Similarity NPC268298

  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 NPC48641 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
0.7528 Intermediate Similarity NPD1698 Clinical (unspecified phase)
0.6897 Remote Similarity NPD1733 Clinical (unspecified phase)
0.6889 Remote Similarity NPD5785 Approved
0.6778 Remote Similarity NPD1695 Approved
0.6768 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6705 Remote Similarity NPD5363 Approved
0.6703 Remote Similarity NPD46 Approved
0.6703 Remote Similarity NPD6698 Approved
0.6667 Remote Similarity NPD7154 Phase 3
0.6629 Remote Similarity NPD5786 Approved
0.6628 Remote Similarity NPD5369 Approved
0.6562 Remote Similarity NPD4225 Approved
0.6552 Remote Similarity NPD4269 Approved
0.6552 Remote Similarity NPD4270 Approved
0.6512 Remote Similarity NPD4252 Approved
0.6512 Remote Similarity NPD5790 Clinical (unspecified phase)
0.6452 Remote Similarity NPD7983 Approved
0.641 Remote Similarity NPD9496 Clinical (unspecified phase)
0.6408 Remote Similarity NPD6371 Approved
0.6364 Remote Similarity NPD5209 Approved
0.6364 Remote Similarity NPD6435 Approved
0.6333 Remote Similarity NPD6082 Clinical (unspecified phase)
0.6333 Remote Similarity NPD1694 Approved
0.6316 Remote Similarity NPD5282 Discontinued
0.6292 Remote Similarity NPD5362 Discontinued
0.6279 Remote Similarity NPD4268 Approved
0.6279 Remote Similarity NPD4271 Approved
0.6264 Remote Similarity NPD4249 Approved
0.6237 Remote Similarity NPD5764 Clinical (unspecified phase)
0.6237 Remote Similarity NPD6101 Approved
0.6211 Remote Similarity NPD5778 Approved
0.6211 Remote Similarity NPD6399 Phase 3
0.6211 Remote Similarity NPD5779 Approved
0.6196 Remote Similarity NPD4250 Approved
0.6196 Remote Similarity NPD4251 Approved
0.618 Remote Similarity NPD4752 Clinical (unspecified phase)
0.6173 Remote Similarity NPD229 Approved
0.617 Remote Similarity NPD7838 Discovery
0.6164 Remote Similarity NPD9298 Approved
0.6136 Remote Similarity NPD5368 Approved
0.6136 Remote Similarity NPD4820 Approved
0.6136 Remote Similarity NPD4819 Approved
0.6136 Remote Similarity NPD4822 Approved
0.6136 Remote Similarity NPD4821 Approved
0.6105 Remote Similarity NPD8034 Phase 2
0.6105 Remote Similarity NPD8035 Phase 2
0.6105 Remote Similarity NPD6411 Approved
0.6064 Remote Similarity NPD5370 Suspended
0.6061 Remote Similarity NPD8029 Clinical (unspecified phase)
0.602 Remote Similarity NPD7839 Suspended
0.5938 Remote Similarity NPD4810 Clinical (unspecified phase)
0.5909 Remote Similarity NPD7115 Discovery
0.5909 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5905 Remote Similarity NPD6686 Approved
0.5888 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5802 Remote Similarity NPD2685 Clinical (unspecified phase)
0.58 Remote Similarity NPD7902 Approved
0.5795 Remote Similarity NPD4756 Discovery
0.5773 Remote Similarity NPD7637 Suspended
0.5761 Remote Similarity NPD5332 Approved
0.5761 Remote Similarity NPD5331 Approved
0.5747 Remote Similarity NPD8039 Approved
0.5745 Remote Similarity NPD6422 Discontinued
0.5714 Remote Similarity NPD4790 Discontinued
0.5702 Remote Similarity NPD8513 Phase 3
0.5702 Remote Similarity NPD8517 Approved
0.5702 Remote Similarity NPD8515 Approved
0.5702 Remote Similarity NPD8516 Approved
0.5699 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5688 Remote Similarity NPD6053 Discontinued
0.5648 Remote Similarity NPD5955 Clinical (unspecified phase)
0.5607 Remote Similarity NPD5345 Clinical (unspecified phase)
0.56 Remote Similarity NPD5695 Phase 3

  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