Structure

Physi-Chem Properties

Molecular Weight:  544.33
Volume:  562.614
LogP:  2.226
LogD:  1.305
LogS:  -3.399
# Rotatable Bonds:  6
TPSA:  110.05
# H-Bond Aceptor:  8
# H-Bond Donor:  1
# Rings:  5
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.544
Synthetic Accessibility Score:  5.281
Fsp3:  0.806
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.997
MDCK Permeability:  1.4202513739292044e-05
Pgp-inhibitor:  0.996
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.108
30% Bioavailability (F30%):  0.953

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.481
Plasma Protein Binding (PPB):  92.79216766357422%
Volume Distribution (VD):  0.302
Pgp-substrate:  9.067527770996094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.009
CYP1A2-substrate:  0.403
CYP2C19-inhibitor:  0.022
CYP2C19-substrate:  0.695
CYP2C9-inhibitor:  0.212
CYP2C9-substrate:  0.487
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.13
CYP3A4-inhibitor:  0.266
CYP3A4-substrate:  0.29

ADMET: Excretion

Clearance (CL):  2.558
Half-life (T1/2):  0.324

ADMET: Toxicity

hERG Blockers:  0.706
Human Hepatotoxicity (H-HT):  0.908
Drug-inuced Liver Injury (DILI):  0.469
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.295
Maximum Recommended Daily Dose:  0.975
Skin Sensitization:  0.497
Carcinogencity:  0.083
Eye Corrosion:  0.004
Eye Irritation:  0.034
Respiratory Toxicity:  0.898

Download Data

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

  Natural Product: NPC321197

Natural Product ID:  NPC321197
Common Name*:   Sodium;2-[(1S,4R,5As,5Br,7As,11As,11Br,13R,13As)-13-Acetyloxy-1,4-Dimethoxy-5B,8,8,11A,13A-Pentamethyl-3-Oxo-4,5,5A,6,7,7A,9,10,11,11B,12,13-Dodecahydro-1H-Phenanthro[2,1-E]Isoindol-2-Yl]Acetate
IUPAC Name:   sodium;2-[(1S,4R,5aS,5bR,7aS,11aS,11bR,13R,13aS)-13-acetyloxy-1,4-dimethoxy-5b,8,8,11a,13a-pentamethyl-3-oxo-4,5,5a,6,7,7a,9,10,11,11b,12,13-dodecahydro-1H-phenanthro[2,1-e]isoindol-2-yl]acetate
Synonyms:  
Standard InCHIKey:  BBHAAZMOYFZRHO-YQLNDFCVSA-M
Standard InCHI:  InChI=1S/C31H47NO7.Na/c1-17(33)39-22-15-20-29(4)12-9-11-28(2,3)19(29)10-13-30(20,5)21-14-18(37-7)24-25(31(21,22)6)27(38-8)32(26(24)36)16-23(34)35;/h18-22,27H,9-16H2,1-8H3,(H,34,35);/q;+1/p-1/t18-,19+,20-,21+,22-,27+,29+,30-,31-;/m1./s1
SMILES:  CC(=O)OC1CC2C3(CCCC(C3CCC2(C4C1(C5=C(C(C4)OC)C(=O)N(C5OC)CC(=O)[O-])C)C)(C)C)C.[Na+]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1773898
PubChem CID:   52951511
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001552] Sesterterpenoids
          • [CHEMONTID:0002883] Scalarane sesterterpenoids

*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
NPO33664 Hyatella sp. Species n.a. n.a. n.a. the coast of Soheuksan-do, Korea n.a. PMID[21341710]
NPO31085 Hyattella Genus Spongiidae Eukaryota n.a. n.a. n.a. PMID[21341710]

☑ 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
NPT111 Cell Line K562 Homo sapiens LC50 = 27000.0 nM PMID[474766]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 50.0 ug.mL-1 PMID[474766]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 6.25 ug.mL-1 PMID[474766]
NPT729 Organism Micrococcus luteus Micrococcus luteus MIC = 25.0 ug.mL-1 PMID[474766]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium MIC = 50.0 ug.mL-1 PMID[474766]
NPT766 Organism Proteus vulgaris Proteus vulgaris MIC = 25.0 ug.mL-1 PMID[474766]
NPT19 Organism Escherichia coli Escherichia coli MIC = 100.0 ug.mL-1 PMID[474766]
NPT2 Others Unspecified IC50 = 176400.0 nM PMID[474766]

☑ 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 NPC321197 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
0.7381 Intermediate Similarity NPC145501
0.7333 Intermediate Similarity NPC165250
0.7258 Intermediate Similarity NPC31522
0.7177 Intermediate Similarity NPC90946
0.7177 Intermediate Similarity NPC300614
0.7143 Intermediate Similarity NPC132753
0.7143 Intermediate Similarity NPC151681
0.7143 Intermediate Similarity NPC121402
0.7143 Intermediate Similarity NPC175351
0.7143 Intermediate Similarity NPC224356
0.7131 Intermediate Similarity NPC471208
0.7131 Intermediate Similarity NPC254202
0.712 Intermediate Similarity NPC218602
0.7059 Intermediate Similarity NPC472362
0.7059 Intermediate Similarity NPC472363
0.7059 Intermediate Similarity NPC154526
0.704 Intermediate Similarity NPC325054
0.7016 Intermediate Similarity NPC476926
0.6947 Remote Similarity NPC9714
0.6905 Remote Similarity NPC189075
0.6905 Remote Similarity NPC476918
0.6905 Remote Similarity NPC275539
0.6884 Remote Similarity NPC478139
0.6861 Remote Similarity NPC478136
0.6855 Remote Similarity NPC159533
0.6855 Remote Similarity NPC95899
0.685 Remote Similarity NPC112457
0.6829 Remote Similarity NPC77703
0.6825 Remote Similarity NPC110496
0.6822 Remote Similarity NPC277769
0.68 Remote Similarity NPC476763
0.68 Remote Similarity NPC476764
0.68 Remote Similarity NPC476921
0.6788 Remote Similarity NPC204556
0.678 Remote Similarity NPC161638
0.678 Remote Similarity NPC8062
0.675 Remote Similarity NPC84893
0.6748 Remote Similarity NPC477964
0.6746 Remote Similarity NPC476761
0.6746 Remote Similarity NPC476762
0.6746 Remote Similarity NPC476760
0.6739 Remote Similarity NPC476957
0.6721 Remote Similarity NPC84335
0.6721 Remote Similarity NPC38530
0.6694 Remote Similarity NPC471075
0.6693 Remote Similarity NPC475570
0.6692 Remote Similarity NPC194951
0.6692 Remote Similarity NPC476956
0.6692 Remote Similarity NPC12046
0.6692 Remote Similarity NPC269530
0.6692 Remote Similarity NPC4573
0.6692 Remote Similarity NPC90952
0.6667 Remote Similarity NPC63511
0.6667 Remote Similarity NPC472666
0.6667 Remote Similarity NPC470277
0.6641 Remote Similarity NPC469597
0.6641 Remote Similarity NPC473483
0.6641 Remote Similarity NPC477963
0.6641 Remote Similarity NPC157441
0.664 Remote Similarity NPC476081
0.664 Remote Similarity NPC295791
0.664 Remote Similarity NPC162973
0.662 Remote Similarity NPC120420
0.6617 Remote Similarity NPC134430
0.6614 Remote Similarity NPC86906
0.6613 Remote Similarity NPC471413
0.6613 Remote Similarity NPC476299
0.6613 Remote Similarity NPC476933
0.6613 Remote Similarity NPC110897
0.6613 Remote Similarity NPC117685
0.6613 Remote Similarity NPC474012
0.6589 Remote Similarity NPC476759
0.6573 Remote Similarity NPC99864
0.6565 Remote Similarity NPC42658
0.656 Remote Similarity NPC93744
0.656 Remote Similarity NPC476888
0.656 Remote Similarity NPC471412
0.6547 Remote Similarity NPC317654
0.6547 Remote Similarity NPC96010
0.6535 Remote Similarity NPC475239
0.6535 Remote Similarity NPC470297
0.6535 Remote Similarity NPC222161
0.6532 Remote Similarity NPC264378
0.6529 Remote Similarity NPC475657
0.6522 Remote Similarity NPC469999
0.6519 Remote Similarity NPC473636
0.6519 Remote Similarity NPC77689
0.6515 Remote Similarity NPC33360
0.6515 Remote Similarity NPC25909
0.6512 Remote Similarity NPC476765
0.6512 Remote Similarity NPC476276
0.6508 Remote Similarity NPC476890
0.6508 Remote Similarity NPC476769
0.6508 Remote Similarity NPC40918
0.6508 Remote Similarity NPC469606
0.6508 Remote Similarity NPC273005
0.6508 Remote Similarity NPC31058
0.6504 Remote Similarity NPC8954
0.6504 Remote Similarity NPC94905
0.6496 Remote Similarity NPC474013
0.6493 Remote Similarity NPC55296
0.6493 Remote Similarity NPC474483
0.6493 Remote Similarity NPC475809
0.6489 Remote Similarity NPC474411
0.6489 Remote Similarity NPC474431
0.6484 Remote Similarity NPC469607
0.6484 Remote Similarity NPC477090
0.648 Remote Similarity NPC54705
0.648 Remote Similarity NPC251680
0.648 Remote Similarity NPC473219
0.648 Remote Similarity NPC476767
0.648 Remote Similarity NPC470761
0.6479 Remote Similarity NPC189393
0.6479 Remote Similarity NPC90814
0.6475 Remote Similarity NPC470697
0.6471 Remote Similarity NPC268530
0.6471 Remote Similarity NPC251226
0.6471 Remote Similarity NPC154491
0.6466 Remote Similarity NPC110861
0.6462 Remote Similarity NPC299590
0.6457 Remote Similarity NPC478057
0.6457 Remote Similarity NPC476889
0.6457 Remote Similarity NPC120321
0.6452 Remote Similarity NPC100912
0.6452 Remote Similarity NPC51499
0.6452 Remote Similarity NPC2049
0.6446 Remote Similarity NPC473944
0.6444 Remote Similarity NPC113448
0.6439 Remote Similarity NPC470063
0.6439 Remote Similarity NPC476163
0.6435 Remote Similarity NPC282293
0.6434 Remote Similarity NPC476111
0.6434 Remote Similarity NPC67321
0.6434 Remote Similarity NPC187435
0.6434 Remote Similarity NPC180744
0.6429 Remote Similarity NPC475527
0.6429 Remote Similarity NPC265699
0.6423 Remote Similarity NPC4021
0.6423 Remote Similarity NPC159456
0.6423 Remote Similarity NPC476204
0.6423 Remote Similarity NPC67569
0.6423 Remote Similarity NPC170084
0.6418 Remote Similarity NPC44170
0.6418 Remote Similarity NPC72772
0.6418 Remote Similarity NPC469794
0.6418 Remote Similarity NPC268954
0.6417 Remote Similarity NPC471043
0.6412 Remote Similarity NPC179642
0.6412 Remote Similarity NPC476766
0.6412 Remote Similarity NPC253906
0.6412 Remote Similarity NPC478209
0.6406 Remote Similarity NPC146731
0.6406 Remote Similarity NPC189616
0.64 Remote Similarity NPC107806
0.64 Remote Similarity NPC325229
0.64 Remote Similarity NPC275086
0.64 Remote Similarity NPC72647
0.64 Remote Similarity NPC176845
0.6397 Remote Similarity NPC230513
0.6397 Remote Similarity NPC42673
0.6397 Remote Similarity NPC473839
0.6397 Remote Similarity NPC211093
0.6397 Remote Similarity NPC475520
0.6393 Remote Similarity NPC271652
0.6393 Remote Similarity NPC7349
0.6393 Remote Similarity NPC199543
0.6391 Remote Similarity NPC159333
0.6391 Remote Similarity NPC470120
0.6389 Remote Similarity NPC76999
0.6387 Remote Similarity NPC113620
0.6387 Remote Similarity NPC100612
0.6387 Remote Similarity NPC174336
0.6387 Remote Similarity NPC175293
0.6387 Remote Similarity NPC187497
0.6387 Remote Similarity NPC475599
0.6385 Remote Similarity NPC474099
0.6385 Remote Similarity NPC151393
0.6385 Remote Similarity NPC89171
0.6385 Remote Similarity NPC476802
0.6378 Remote Similarity NPC80781
0.6378 Remote Similarity NPC137430
0.6377 Remote Similarity NPC23786
0.6377 Remote Similarity NPC470265
0.6377 Remote Similarity NPC269642
0.6371 Remote Similarity NPC7124
0.6371 Remote Similarity NPC194132
0.6371 Remote Similarity NPC242848
0.6371 Remote Similarity NPC134072
0.6371 Remote Similarity NPC234993
0.6371 Remote Similarity NPC29952
0.6371 Remote Similarity NPC209297
0.6371 Remote Similarity NPC475380
0.637 Remote Similarity NPC473968
0.6364 Remote Similarity NPC58281
0.6364 Remote Similarity NPC79238
0.6364 Remote Similarity NPC475776
0.6364 Remote Similarity NPC120335
0.6364 Remote Similarity NPC47230
0.6364 Remote Similarity NPC17143
0.6364 Remote Similarity NPC324683

  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 NPC321197 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
0.7165 Intermediate Similarity NPD1376 Discontinued
0.6667 Remote Similarity NPD6908 Approved
0.6667 Remote Similarity NPD6909 Approved
0.6643 Remote Similarity NPD8387 Clinical (unspecified phase)
0.6573 Remote Similarity NPD8415 Approved
0.6562 Remote Similarity NPD5954 Clinical (unspecified phase)
0.6532 Remote Similarity NPD7638 Approved
0.648 Remote Similarity NPD7640 Approved
0.648 Remote Similarity NPD7639 Approved
0.6462 Remote Similarity NPD4061 Clinical (unspecified phase)
0.6434 Remote Similarity NPD6845 Suspended
0.6412 Remote Similarity NPD5955 Clinical (unspecified phase)
0.6378 Remote Similarity NPD7632 Discontinued
0.6371 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6364 Remote Similarity NPD7260 Phase 2
0.6341 Remote Similarity NPD7901 Clinical (unspecified phase)
0.6341 Remote Similarity NPD7900 Approved
0.6327 Remote Similarity NPD6334 Approved
0.6327 Remote Similarity NPD6333 Approved
0.6304 Remote Similarity NPD6921 Approved
0.621 Remote Similarity NPD7748 Approved
0.62 Remote Similarity NPD8384 Approved
0.619 Remote Similarity NPD7902 Approved
0.6181 Remote Similarity NPD6914 Discontinued
0.6154 Remote Similarity NPD8336 Approved
0.6154 Remote Similarity NPD8337 Approved
0.6131 Remote Similarity NPD7115 Discovery
0.6111 Remote Similarity NPD7319 Approved
0.6107 Remote Similarity NPD6008 Approved
0.6107 Remote Similarity NPD7333 Discontinued
0.6102 Remote Similarity NPD4752 Clinical (unspecified phase)
0.6096 Remote Similarity NPD8338 Approved
0.6066 Remote Similarity NPD7513 Clinical (unspecified phase)
0.6048 Remote Similarity NPD7515 Phase 2
0.6015 Remote Similarity NPD6686 Approved
0.6014 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6014 Remote Similarity NPD7507 Approved
0.595 Remote Similarity NPD1694 Approved
0.5915 Remote Similarity NPD8080 Discontinued
0.5912 Remote Similarity NPD8298 Phase 2
0.5903 Remote Similarity NPD8273 Phase 1
0.5902 Remote Similarity NPD7521 Approved
0.5902 Remote Similarity NPD6684 Approved
0.5902 Remote Similarity NPD6409 Approved
0.5902 Remote Similarity NPD5330 Approved
0.5902 Remote Similarity NPD7146 Approved
0.5902 Remote Similarity NPD7334 Approved
0.5899 Remote Similarity NPD8295 Clinical (unspecified phase)
0.5891 Remote Similarity NPD4225 Approved
0.5882 Remote Similarity NPD2204 Approved
0.5873 Remote Similarity NPD6399 Phase 3
0.5845 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5812 Remote Similarity NPD8143 Approved
0.5812 Remote Similarity NPD8144 Approved
0.5806 Remote Similarity NPD5737 Approved
0.5806 Remote Similarity NPD6672 Approved
0.5806 Remote Similarity NPD6903 Approved
0.5802 Remote Similarity NPD8414 Discontinued
0.5794 Remote Similarity NPD8034 Phase 2
0.5794 Remote Similarity NPD8035 Phase 2
0.5764 Remote Similarity NPD7604 Phase 2
0.5764 Remote Similarity NPD8328 Phase 3
0.5764 Remote Similarity NPD7642 Approved
0.5764 Remote Similarity NPD7122 Discontinued
0.5746 Remote Similarity NPD6675 Approved
0.5746 Remote Similarity NPD6402 Approved
0.5746 Remote Similarity NPD5739 Approved
0.5746 Remote Similarity NPD7128 Approved
0.5745 Remote Similarity NPD7327 Approved
0.5745 Remote Similarity NPD7328 Approved
0.5743 Remote Similarity NPD8391 Approved
0.5743 Remote Similarity NPD8392 Approved
0.5743 Remote Similarity NPD8390 Approved
0.5736 Remote Similarity NPD7732 Phase 3
0.5735 Remote Similarity NPD8132 Clinical (unspecified phase)
0.5734 Remote Similarity NPD8033 Approved
0.5726 Remote Similarity NPD3573 Approved
0.5714 Remote Similarity NPD7736 Approved
0.5704 Remote Similarity NPD7516 Approved
0.5685 Remote Similarity NPD8451 Approved
0.5669 Remote Similarity NPD5693 Phase 1
0.5664 Remote Similarity NPD8294 Approved
0.5664 Remote Similarity NPD6319 Approved
0.5664 Remote Similarity NPD8377 Approved
0.5662 Remote Similarity NPD7320 Approved
0.5662 Remote Similarity NPD6881 Approved
0.5662 Remote Similarity NPD6899 Approved
0.5662 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5659 Remote Similarity NPD7991 Discontinued
0.5659 Remote Similarity NPD6356 Clinical (unspecified phase)
0.5646 Remote Similarity NPD8448 Approved
0.563 Remote Similarity NPD8040 Discontinued
0.563 Remote Similarity NPD6920 Discontinued
0.5625 Remote Similarity NPD8380 Approved
0.5625 Remote Similarity NPD8296 Approved
0.5625 Remote Similarity NPD8379 Approved
0.5625 Remote Similarity NPD8335 Approved
0.5625 Remote Similarity NPD8378 Approved
0.562 Remote Similarity NPD6372 Approved
0.562 Remote Similarity NPD6373 Approved
0.5616 Remote Similarity NPD7492 Approved
0.5612 Remote Similarity NPD8078 Approved
0.5612 Remote Similarity NPD8077 Approved
0.5612 Remote Similarity NPD6053 Discontinued

  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