Structure

Physi-Chem Properties

Molecular Weight:  421.25
Volume:  445.727
LogP:  3.391
LogD:  2.206
LogS:  -3.391
# Rotatable Bonds:  12
TPSA:  121.1
# H-Bond Aceptor:  7
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.298
Synthetic Accessibility Score:  4.43
Fsp3:  0.696
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.251
MDCK Permeability:  1.5672076187911443e-05
Pgp-inhibitor:  0.929
Pgp-substrate:  0.131
Human Intestinal Absorption (HIA):  0.586
20% Bioavailability (F20%):  0.555
30% Bioavailability (F30%):  0.229

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.296
Plasma Protein Binding (PPB):  93.32130432128906%
Volume Distribution (VD):  0.271
Pgp-substrate:  5.627103328704834%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.147
CYP2C19-inhibitor:  0.03
CYP2C19-substrate:  0.266
CYP2C9-inhibitor:  0.052
CYP2C9-substrate:  0.979
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.075
CYP3A4-inhibitor:  0.027
CYP3A4-substrate:  0.147

ADMET: Excretion

Clearance (CL):  5.381
Half-life (T1/2):  0.859

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.628
Drug-inuced Liver Injury (DILI):  0.929
AMES Toxicity:  0.049
Rat Oral Acute Toxicity:  0.136
Maximum Recommended Daily Dose:  0.04
Skin Sensitization:  0.319
Carcinogencity:  0.134
Eye Corrosion:  0.004
Eye Irritation:  0.027
Respiratory Toxicity:  0.16

Download Data

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

  Natural Product: NPC472615

Natural Product ID:  NPC472615
Common Name*:   BYLZXAMDXFCHOS-NMAXYDGISA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BYLZXAMDXFCHOS-NMAXYDGISA-N
Standard InCHI:  InChI=1S/C23H35NO6/c1-15(2)11-17(4)12-16(3)8-9-21(27)24-18-14-23(30,20(26)13-19(18)25)10-6-5-7-22(28)29/h8-9,11,14,16-17,20,26,30H,5-7,10,12-13H2,1-4H3,(H,24,27)(H,28,29)/b9-8+/t16-,17+,20+,23-/m1/s1
SMILES:  CC(CC(C)C=C(C)C)C=CC(=O)NC1=CC(C(CC1=O)O)(CCCCC(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3581259
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001563] Monocyclic monoterpenoids

*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
NPO33196 streptomyces sp. actinobacterium Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[25700232]

☑ 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
NPT82 Cell Line MDA-MB-231 Homo sapiens IC50 > 100000.0 nM PMID[479471]
NPT111 Cell Line K562 Homo sapiens IC50 > 100000.0 nM PMID[479471]
NPT393 Cell Line HCT-116 Homo sapiens IC50 > 100000.0 nM PMID[479471]
NPT81 Cell Line A549 Homo sapiens IC50 > 100000.0 nM PMID[479471]
NPT2 Others Unspecified IC50 > 100000.0 nM PMID[479471]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 100000.0 nM PMID[479471]

☑ 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 NPC472615 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
0.9694 High Similarity NPC472616
0.8585 High Similarity NPC133729
0.8351 Intermediate Similarity NPC472614
0.8056 Intermediate Similarity NPC251330
0.7963 Intermediate Similarity NPC271269
0.7941 Intermediate Similarity NPC472613
0.7739 Intermediate Similarity NPC316325
0.7658 Intermediate Similarity NPC307903
0.7658 Intermediate Similarity NPC140251
0.7636 Intermediate Similarity NPC154601
0.7632 Intermediate Similarity NPC5485
0.7586 Intermediate Similarity NPC59751
0.7586 Intermediate Similarity NPC27413
0.7586 Intermediate Similarity NPC271621
0.75 Intermediate Similarity NPC315652
0.75 Intermediate Similarity NPC7905
0.7456 Intermediate Similarity NPC170375
0.7407 Intermediate Similarity NPC234542
0.74 Intermediate Similarity NPC477786
0.74 Intermediate Similarity NPC477784
0.74 Intermediate Similarity NPC477785
0.7395 Intermediate Similarity NPC473808
0.7373 Intermediate Similarity NPC296361
0.7339 Intermediate Similarity NPC473224
0.7333 Intermediate Similarity NPC315915
0.7297 Intermediate Similarity NPC474563
0.7213 Intermediate Similarity NPC16709
0.7119 Intermediate Similarity NPC471645
0.708 Intermediate Similarity NPC14537
0.7064 Intermediate Similarity NPC175614
0.704 Intermediate Similarity NPC473249
0.7031 Intermediate Similarity NPC314361
0.7018 Intermediate Similarity NPC473252
0.7009 Intermediate Similarity NPC142838
0.6975 Remote Similarity NPC476813
0.6975 Remote Similarity NPC476814
0.6964 Remote Similarity NPC316250
0.6952 Remote Similarity NPC472007
0.6949 Remote Similarity NPC469865
0.6923 Remote Similarity NPC122926
0.6923 Remote Similarity NPC261380
0.6923 Remote Similarity NPC113012
0.6916 Remote Similarity NPC265856
0.6916 Remote Similarity NPC166554
0.6903 Remote Similarity NPC128501
0.69 Remote Similarity NPC192006
0.69 Remote Similarity NPC231739
0.6881 Remote Similarity NPC65829
0.6863 Remote Similarity NPC474980
0.6857 Remote Similarity NPC315395
0.6857 Remote Similarity NPC316426
0.6857 Remote Similarity NPC258824
0.6857 Remote Similarity NPC472009
0.6852 Remote Similarity NPC314500
0.6846 Remote Similarity NPC78189
0.6818 Remote Similarity NPC230889
0.6807 Remote Similarity NPC476269
0.68 Remote Similarity NPC471061
0.6796 Remote Similarity NPC85772
0.6796 Remote Similarity NPC7414
0.6789 Remote Similarity NPC469692
0.6789 Remote Similarity NPC469645
0.6762 Remote Similarity NPC11804
0.6762 Remote Similarity NPC187529
0.6762 Remote Similarity NPC125290
0.6759 Remote Similarity NPC471399
0.6754 Remote Similarity NPC469598
0.6733 Remote Similarity NPC478122
0.6733 Remote Similarity NPC121200
0.6731 Remote Similarity NPC471595
0.6731 Remote Similarity NPC161045
0.6731 Remote Similarity NPC16488
0.6729 Remote Similarity NPC472008
0.6727 Remote Similarity NPC121825
0.6727 Remote Similarity NPC116930
0.6721 Remote Similarity NPC475642
0.6719 Remote Similarity NPC477793
0.6719 Remote Similarity NPC329919
0.6699 Remote Similarity NPC47031
0.6698 Remote Similarity NPC476982
0.6696 Remote Similarity NPC476344
0.6696 Remote Similarity NPC40812
0.6695 Remote Similarity NPC473578
0.6694 Remote Similarity NPC50694
0.6667 Remote Similarity NPC150041
0.6667 Remote Similarity NPC475800
0.6667 Remote Similarity NPC113363
0.6667 Remote Similarity NPC316249
0.6667 Remote Similarity NPC70424
0.6667 Remote Similarity NPC243618
0.6667 Remote Similarity NPC315531
0.6641 Remote Similarity NPC204556
0.664 Remote Similarity NPC475383
0.664 Remote Similarity NPC156379
0.6639 Remote Similarity NPC476290
0.6639 Remote Similarity NPC30196
0.6637 Remote Similarity NPC187761
0.6637 Remote Similarity NPC83895
0.6636 Remote Similarity NPC471738
0.6636 Remote Similarity NPC72513
0.6634 Remote Similarity NPC281296
0.6614 Remote Similarity NPC469494
0.6614 Remote Similarity NPC204639
0.661 Remote Similarity NPC475150
0.6609 Remote Similarity NPC39996
0.6607 Remote Similarity NPC473291
0.6607 Remote Similarity NPC123141
0.6606 Remote Similarity NPC145666
0.6606 Remote Similarity NPC473448
0.6604 Remote Similarity NPC137033
0.6604 Remote Similarity NPC28887
0.6602 Remote Similarity NPC115418
0.66 Remote Similarity NPC199445
0.6585 Remote Similarity NPC476190
0.6585 Remote Similarity NPC201968
0.6585 Remote Similarity NPC6531
0.6583 Remote Similarity NPC21713
0.6583 Remote Similarity NPC475608
0.6583 Remote Similarity NPC12270
0.6574 Remote Similarity NPC476803
0.6574 Remote Similarity NPC316186
0.6569 Remote Similarity NPC475994
0.6565 Remote Similarity NPC96425
0.6555 Remote Similarity NPC474725
0.6552 Remote Similarity NPC475050
0.6549 Remote Similarity NPC265662
0.6549 Remote Similarity NPC20066
0.6545 Remote Similarity NPC261607
0.6545 Remote Similarity NPC300312
0.6545 Remote Similarity NPC111114
0.6545 Remote Similarity NPC476705
0.6542 Remote Similarity NPC469483
0.6542 Remote Similarity NPC261721
0.6542 Remote Similarity NPC164393
0.6542 Remote Similarity NPC469910
0.6538 Remote Similarity NPC275766
0.6535 Remote Similarity NPC279537
0.6525 Remote Similarity NPC469853
0.6522 Remote Similarity NPC46998
0.6522 Remote Similarity NPC185141
0.6522 Remote Similarity NPC110443
0.6522 Remote Similarity NPC128733
0.6522 Remote Similarity NPC115862
0.6522 Remote Similarity NPC133907
0.6518 Remote Similarity NPC54905
0.6518 Remote Similarity NPC272050
0.6518 Remote Similarity NPC314009
0.6514 Remote Similarity NPC477215
0.6514 Remote Similarity NPC476388
0.6514 Remote Similarity NPC212598
0.6509 Remote Similarity NPC9868
0.6509 Remote Similarity NPC472326
0.6508 Remote Similarity NPC469515
0.6505 Remote Similarity NPC164308
0.6505 Remote Similarity NPC201225
0.65 Remote Similarity NPC160540
0.65 Remote Similarity NPC477997
0.65 Remote Similarity NPC29133
0.6496 Remote Similarity NPC74035
0.6491 Remote Similarity NPC316598
0.6491 Remote Similarity NPC261377
0.6491 Remote Similarity NPC300584
0.6491 Remote Similarity NPC255592
0.6491 Remote Similarity NPC161855
0.6491 Remote Similarity NPC308567
0.6481 Remote Similarity NPC179659
0.6481 Remote Similarity NPC86005
0.648 Remote Similarity NPC241050
0.6476 Remote Similarity NPC474291
0.6476 Remote Similarity NPC475690
0.6471 Remote Similarity NPC70235
0.6462 Remote Similarity NPC471586
0.646 Remote Similarity NPC165332
0.646 Remote Similarity NPC180722
0.646 Remote Similarity NPC195645
0.6455 Remote Similarity NPC313670
0.6455 Remote Similarity NPC476004
0.6455 Remote Similarity NPC477684
0.6455 Remote Similarity NPC316228
0.6455 Remote Similarity NPC474761
0.6449 Remote Similarity NPC470755
0.6446 Remote Similarity NPC470961
0.6446 Remote Similarity NPC29501
0.6442 Remote Similarity NPC470946
0.6442 Remote Similarity NPC271104
0.6442 Remote Similarity NPC470945
0.6442 Remote Similarity NPC470947
0.6441 Remote Similarity NPC469852
0.6436 Remote Similarity NPC60718
0.6429 Remote Similarity NPC472976
0.6429 Remote Similarity NPC167219
0.6429 Remote Similarity NPC233770
0.6429 Remote Similarity NPC53685
0.6429 Remote Similarity NPC472977
0.6429 Remote Similarity NPC5418
0.6429 Remote Similarity NPC77481
0.6423 Remote Similarity NPC67259
0.6423 Remote Similarity NPC147912
0.6422 Remote Similarity NPC476805
0.6422 Remote Similarity NPC476708

  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 NPC472615 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
0.7928 Intermediate Similarity NPD7116 Clinical (unspecified phase)
0.7739 Intermediate Similarity NPD7500 Approved
0.7456 Intermediate Similarity NPD7601 Clinical (unspecified phase)
0.7273 Intermediate Similarity NPD7623 Phase 3
0.7273 Intermediate Similarity NPD7624 Clinical (unspecified phase)
0.7087 Intermediate Similarity NPD5363 Approved
0.7049 Intermediate Similarity NPD7739 Clinical (unspecified phase)
0.704 Intermediate Similarity NPD7747 Phase 1
0.704 Intermediate Similarity NPD7746 Phase 1
0.6838 Remote Similarity NPD6413 Approved
0.6829 Remote Similarity NPD7299 Clinical (unspecified phase)
0.6796 Remote Similarity NPD4270 Approved
0.6796 Remote Similarity NPD4269 Approved
0.6759 Remote Similarity NPD5785 Approved
0.6639 Remote Similarity NPD6421 Discontinued
0.6639 Remote Similarity NPD6420 Discontinued
0.6602 Remote Similarity NPD4252 Approved
0.6583 Remote Similarity NPD1719 Phase 1
0.6542 Remote Similarity NPD5786 Approved
0.6538 Remote Similarity NPD5369 Approved
0.646 Remote Similarity NPD7839 Suspended
0.6452 Remote Similarity NPD7505 Discontinued
0.6408 Remote Similarity NPD3732 Approved
0.6396 Remote Similarity NPD7983 Approved
0.6339 Remote Similarity NPD5779 Approved
0.6339 Remote Similarity NPD5778 Approved
0.632 Remote Similarity NPD7115 Discovery
0.6306 Remote Similarity NPD6698 Approved
0.6306 Remote Similarity NPD46 Approved
0.6293 Remote Similarity NPD6404 Discontinued
0.6279 Remote Similarity NPD7642 Approved
0.6262 Remote Similarity NPD7154 Phase 3
0.6262 Remote Similarity NPD5362 Discontinued
0.626 Remote Similarity NPD8074 Phase 3
0.625 Remote Similarity NPD5784 Clinical (unspecified phase)
0.623 Remote Similarity NPD6371 Approved
0.6142 Remote Similarity NPD7641 Discontinued
0.6134 Remote Similarity NPD2259 Approved
0.6134 Remote Similarity NPD2258 Approved
0.6132 Remote Similarity NPD4820 Approved
0.6132 Remote Similarity NPD4822 Approved
0.6132 Remote Similarity NPD4819 Approved
0.6132 Remote Similarity NPD4821 Approved
0.6106 Remote Similarity NPD4810 Clinical (unspecified phase)
0.6087 Remote Similarity NPD1698 Clinical (unspecified phase)
0.608 Remote Similarity NPD1376 Discontinued
0.6071 Remote Similarity NPD5370 Suspended
0.6071 Remote Similarity NPD6101 Approved
0.6071 Remote Similarity NPD5764 Clinical (unspecified phase)
0.6068 Remote Similarity NPD4225 Approved
0.6068 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6061 Remote Similarity NPD8273 Phase 1
0.6053 Remote Similarity NPD5781 Clinical (unspecified phase)
0.6043 Remote Similarity NPD6334 Approved
0.6043 Remote Similarity NPD6333 Approved
0.6034 Remote Similarity NPD4228 Discovery
0.6 Remote Similarity NPD4756 Discovery
0.5985 Remote Similarity NPD8341 Approved
0.5985 Remote Similarity NPD8340 Approved
0.5985 Remote Similarity NPD8299 Approved
0.5985 Remote Similarity NPD8342 Approved
0.5984 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5965 Remote Similarity NPD6411 Approved
0.5963 Remote Similarity NPD5331 Approved
0.5963 Remote Similarity NPD5332 Approved
0.596 Remote Similarity NPD7331 Phase 2
0.5943 Remote Similarity NPD4268 Approved
0.5943 Remote Similarity NPD4271 Approved
0.5926 Remote Similarity NPD4790 Discontinued
0.5909 Remote Similarity NPD7830 Approved
0.5909 Remote Similarity NPD7829 Approved
0.5882 Remote Similarity NPD6914 Discontinued
0.5877 Remote Similarity NPD7838 Discovery
0.5833 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5833 Remote Similarity NPD5368 Approved
0.5826 Remote Similarity NPD7515 Phase 2
0.5821 Remote Similarity NPD8451 Approved
0.5818 Remote Similarity NPD6110 Phase 1
0.5778 Remote Similarity NPD8448 Approved
0.5766 Remote Similarity NPD8392 Approved
0.5766 Remote Similarity NPD8390 Approved
0.5766 Remote Similarity NPD8391 Approved
0.5758 Remote Similarity NPD8444 Approved
0.5758 Remote Similarity NPD3197 Phase 1
0.5727 Remote Similarity NPD6435 Approved
0.5727 Remote Similarity NPD4800 Clinical (unspecified phase)
0.5726 Remote Similarity NPD5282 Discontinued
0.5714 Remote Similarity NPD1694 Approved
0.5714 Remote Similarity NPD2838 Clinical (unspecified phase)
0.5702 Remote Similarity NPD5344 Discontinued
0.57 Remote Similarity NPD7341 Phase 2
0.5692 Remote Similarity NPD6935 Phase 3
0.5692 Remote Similarity NPD6936 Clinical (unspecified phase)
0.569 Remote Similarity NPD7637 Suspended
0.5688 Remote Similarity NPD8259 Clinical (unspecified phase)
0.5669 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5649 Remote Similarity NPD6918 Phase 1
0.5648 Remote Similarity NPD7917 Clinical (unspecified phase)
0.5648 Remote Similarity NPD7918 Clinical (unspecified phase)
0.5645 Remote Similarity NPD4211 Phase 1
0.5641 Remote Similarity NPD6399 Phase 3
0.5639 Remote Similarity NPD8515 Approved
0.5639 Remote Similarity NPD8517 Approved
0.5639 Remote Similarity NPD8516 Approved
0.5639 Remote Similarity NPD8513 Phase 3
0.5612 Remote Similarity NPD7260 Phase 2
0.5603 Remote Similarity NPD8415 Approved
0.5603 Remote Similarity NPD6095 Approved
0.5603 Remote Similarity NPD6094 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