Structure

Physi-Chem Properties

Molecular Weight:  672.31
Volume:  624.88
LogP:  -4.188
LogD:  -3.0
LogS:  -0.447
# Rotatable Bonds:  7
TPSA:  329.06
# H-Bond Aceptor:  20
# H-Bond Donor:  13
# Rings:  3
# Heavy Atoms:  20

MedChem Properties

QED Drug-Likeness Score:  0.12
Synthetic Accessibility Score:  6.339
Fsp3:  0.741
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.956
MDCK Permeability:  0.0006892208475619555
Pgp-inhibitor:  0.0
Pgp-substrate:  1.0
Human Intestinal Absorption (HIA):  0.656
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.249
Plasma Protein Binding (PPB):  20.683979034423828%
Volume Distribution (VD):  0.419
Pgp-substrate:  81.80693817138672%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.002
CYP2C19-inhibitor:  0.004
CYP2C19-substrate:  0.029
CYP2C9-inhibitor:  0.003
CYP2C9-substrate:  0.037
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.028
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.0

ADMET: Excretion

Clearance (CL):  1.116
Half-life (T1/2):  0.649

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.997
Drug-inuced Liver Injury (DILI):  0.651
AMES Toxicity:  0.048
Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.066
Skin Sensitization:  0.355
Carcinogencity:  0.022
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.557

Download Data

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

  Natural Product: NPC275715

Natural Product ID:  NPC275715
Common Name*:   Serinocyclin A
IUPAC Name:   (6S,9R,16R,19S,22S,24R)-16-[(2S)-4-amino-2-hydroxybutyl]-24-hydroxy-6,9,19-tris(hydroxymethyl)spiro[1,4,7,10,14,17,20-heptazabicyclo[20.3.0]pentacosane-3,1'-cyclopropane]-2,5,8,11,15,18,21-heptone
Synonyms:  
Standard InCHIKey:  RBBMDAKGTMLVAP-LPJTWDLVSA-N
Standard InCHI:  InChI=1S/C27H44N8O12/c28-5-1-13(39)7-15-21(42)29-6-2-20(41)30-16(10-36)22(43)32-18(12-38)24(45)34-27(3-4-27)26(47)35-9-14(40)8-19(35)25(46)33-17(11-37)23(44)31-15/h13-19,36-40H,1-12,28H2,(H,29,42)(H,30,41)(H,31,44)(H,32,43)(H,33,46)(H,34,45)/t13-,14+,15+,16+,17-,18-,19-/m0/s1
SMILES:  C(CN)[C@@H](C[C@@H]1C(=NCCC(=N[C@H](CO)C(=N[C@@H](CO)C(=NC2(CC2)C(=O)N2C[C@@H](C[C@H]2C(=N[C@@H](CO)C(=N1)O)O)O)O)O)O)O)O
Synthetic Gene Cluster:   BGC0001240;
ChEMBL Identifier:   CHEMBL269595
PubChem CID:   24762344
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0001813] Peptidomimetics
        • [CHEMONTID:0002010] Hybrid peptides

*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
NPO9967 Metarhizium anisopliae Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[10650095]
NPO9967 Metarhizium anisopliae Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[18044842]
NPO9967 Metarhizium anisopliae Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[20233596]
NPO9967 Metarhizium anisopliae Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[7623030]
NPO9967 Metarhizium anisopliae Species Clavicipitaceae 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
NPT1381 Organism Aedes aegypti Aedes aegypti EC50 = 59.0 ppm PMID[459912]

☑ 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 NPC275715 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
0.7931 Intermediate Similarity NPC476302
0.7907 Intermediate Similarity NPC31756
0.7816 Intermediate Similarity NPC476137
0.7816 Intermediate Similarity NPC476117
0.7816 Intermediate Similarity NPC476156
0.7816 Intermediate Similarity NPC476243
0.78 Intermediate Similarity NPC128303
0.7723 Intermediate Similarity NPC241394
0.7356 Intermediate Similarity NPC470782
0.7333 Intermediate Similarity NPC470783
0.7326 Intermediate Similarity NPC126186
0.7312 Intermediate Similarity NPC477539
0.7273 Intermediate Similarity NPC134504
0.7273 Intermediate Similarity NPC47076
0.7129 Intermediate Similarity NPC475440
0.71 Intermediate Similarity NPC473597
0.7019 Intermediate Similarity NPC476877
0.701 Intermediate Similarity NPC475801
0.701 Intermediate Similarity NPC474593
0.6957 Remote Similarity NPC475542
0.6939 Remote Similarity NPC474576
0.6909 Remote Similarity NPC63191
0.6909 Remote Similarity NPC471202
0.6897 Remote Similarity NPC470781
0.6887 Remote Similarity NPC476876
0.6869 Remote Similarity NPC471098
0.6869 Remote Similarity NPC173763
0.6869 Remote Similarity NPC62263
0.6786 Remote Similarity NPC296043
0.6768 Remote Similarity NPC477538
0.6739 Remote Similarity NPC312315
0.6726 Remote Similarity NPC329216
0.6705 Remote Similarity NPC196007
0.6705 Remote Similarity NPC76297
0.6705 Remote Similarity NPC214532
0.6635 Remote Similarity NPC220234
0.6609 Remote Similarity NPC469899
0.6577 Remote Similarity NPC476875
0.6574 Remote Similarity NPC475637
0.6556 Remote Similarity NPC266888
0.6556 Remote Similarity NPC256312
0.6556 Remote Similarity NPC209156
0.6556 Remote Similarity NPC161774
0.6552 Remote Similarity NPC470652
0.6526 Remote Similarity NPC53858
0.6526 Remote Similarity NPC84128
0.6512 Remote Similarity NPC128005
0.6512 Remote Similarity NPC84182
0.6496 Remote Similarity NPC160688
0.6476 Remote Similarity NPC475758
0.6455 Remote Similarity NPC207820
0.6449 Remote Similarity NPC301148
0.6449 Remote Similarity NPC124554
0.6449 Remote Similarity NPC5864
0.6415 Remote Similarity NPC13175
0.6415 Remote Similarity NPC475791
0.6389 Remote Similarity NPC198344
0.6387 Remote Similarity NPC50520
0.6373 Remote Similarity NPC315237
0.6356 Remote Similarity NPC315188
0.6353 Remote Similarity NPC243964
0.6344 Remote Similarity NPC59867
0.6333 Remote Similarity NPC470654
0.6333 Remote Similarity NPC470650
0.6333 Remote Similarity NPC470653
0.633 Remote Similarity NPC323720
0.633 Remote Similarity NPC124549
0.6325 Remote Similarity NPC477237
0.6306 Remote Similarity NPC67009
0.6304 Remote Similarity NPC327272
0.6296 Remote Similarity NPC475149
0.6296 Remote Similarity NPC471097
0.6292 Remote Similarity NPC322274
0.6264 Remote Similarity NPC474468
0.625 Remote Similarity NPC314466
0.6224 Remote Similarity NPC472351
0.6218 Remote Similarity NPC477238
0.6196 Remote Similarity NPC320221
0.619 Remote Similarity NPC117829
0.6179 Remote Similarity NPC470655
0.6179 Remote Similarity NPC470651
0.6161 Remote Similarity NPC171734
0.6154 Remote Similarity NPC301010
0.6136 Remote Similarity NPC287693
0.6122 Remote Similarity NPC235078
0.61 Remote Similarity NPC469363
0.6095 Remote Similarity NPC280066
0.6082 Remote Similarity NPC23984
0.6047 Remote Similarity NPC8087
0.6047 Remote Similarity NPC62507
0.6023 Remote Similarity NPC262615
0.602 Remote Similarity NPC184473
0.6018 Remote Similarity NPC296143
0.6 Remote Similarity NPC250953
0.5983 Remote Similarity NPC259586
0.5938 Remote Similarity NPC37681
0.5934 Remote Similarity NPC472579
0.5932 Remote Similarity NPC222481
0.5932 Remote Similarity NPC470621
0.5922 Remote Similarity NPC322966
0.5914 Remote Similarity NPC55274
0.5914 Remote Similarity NPC29326
0.5913 Remote Similarity NPC251122
0.5889 Remote Similarity NPC196359
0.5889 Remote Similarity NPC221764
0.5889 Remote Similarity NPC78312
0.5889 Remote Similarity NPC135539
0.5872 Remote Similarity NPC475188
0.587 Remote Similarity NPC473710
0.587 Remote Similarity NPC475694
0.5862 Remote Similarity NPC314510
0.5862 Remote Similarity NPC57846
0.5862 Remote Similarity NPC30126
0.5862 Remote Similarity NPC474014
0.5843 Remote Similarity NPC474928
0.5833 Remote Similarity NPC329077
0.5804 Remote Similarity NPC314398
0.5804 Remote Similarity NPC314413
0.5804 Remote Similarity NPC239705
0.5783 Remote Similarity NPC272396
0.5778 Remote Similarity NPC116377
0.5778 Remote Similarity NPC77191
0.5778 Remote Similarity NPC69798
0.5778 Remote Similarity NPC101746
0.5778 Remote Similarity NPC473952
0.5765 Remote Similarity NPC10262
0.5765 Remote Similarity NPC65832
0.5765 Remote Similarity NPC311668
0.5752 Remote Similarity NPC62845
0.5752 Remote Similarity NPC166242
0.5752 Remote Similarity NPC322449
0.5752 Remote Similarity NPC92874
0.5752 Remote Similarity NPC189854
0.5747 Remote Similarity NPC263207
0.5726 Remote Similarity NPC325750
0.5714 Remote Similarity NPC477729
0.5714 Remote Similarity NPC141156
0.5714 Remote Similarity NPC275727
0.5714 Remote Similarity NPC184150
0.5702 Remote Similarity NPC325900
0.5702 Remote Similarity NPC10897
0.57 Remote Similarity NPC6902
0.57 Remote Similarity NPC246005
0.5699 Remote Similarity NPC478256
0.568 Remote Similarity NPC36254
0.5667 Remote Similarity NPC160661
0.5667 Remote Similarity NPC41429
0.5652 Remote Similarity NPC254617
0.5652 Remote Similarity NPC474469
0.5652 Remote Similarity NPC74555
0.5652 Remote Similarity NPC266242
0.5652 Remote Similarity NPC306763
0.5632 Remote Similarity NPC292299
0.5632 Remote Similarity NPC34838
0.5632 Remote Similarity NPC320598
0.5612 Remote Similarity NPC325902
0.5612 Remote Similarity NPC191774
0.5604 Remote Similarity NPC12514
0.5604 Remote Similarity NPC294883

  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 NPC275715 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
0.8085 Intermediate Similarity NPD7841 Clinical (unspecified phase)
0.8043 Intermediate Similarity NPD4261 Phase 1
0.7912 Intermediate Similarity NPD3177 Phase 3
0.7732 Intermediate Similarity NPD8038 Phase 2
0.7312 Intermediate Similarity NPD7759 Phase 2
0.7312 Intermediate Similarity NPD7760 Phase 2
0.7312 Intermediate Similarity NPD3723 Clinical (unspecified phase)
0.7253 Intermediate Similarity NPD2683 Discontinued
0.7113 Intermediate Similarity NPD4780 Clinical (unspecified phase)
0.6957 Remote Similarity NPD7763 Phase 2
0.6957 Remote Similarity NPD7762 Phase 2
0.6702 Remote Similarity NPD1125 Discovery
0.6667 Remote Similarity NPD6937 Approved
0.6571 Remote Similarity NPD6120 Clinical (unspecified phase)
0.6542 Remote Similarity NPD6122 Discontinued
0.6495 Remote Similarity NPD9401 Discovery
0.6392 Remote Similarity NPD3733 Clinical (unspecified phase)
0.6122 Remote Similarity NPD4829 Discontinued
0.6117 Remote Similarity NPD5792 Clinical (unspecified phase)
0.6111 Remote Similarity NPD620 Approved
0.6091 Remote Similarity NPD8045 Clinical (unspecified phase)
0.6075 Remote Similarity NPD3715 Approved
0.6075 Remote Similarity NPD3713 Approved
0.6075 Remote Similarity NPD3714 Approved
0.6058 Remote Similarity NPD6699 Clinical (unspecified phase)
0.6023 Remote Similarity NPD6438 Approved
0.6023 Remote Similarity NPD6437 Approved
0.6 Remote Similarity NPD322 Phase 1
0.6 Remote Similarity NPD8951 Approved
0.598 Remote Similarity NPD867 Phase 3
0.598 Remote Similarity NPD868 Phase 3
0.5962 Remote Similarity NPD2682 Approved
0.5952 Remote Similarity NPD9425 Approved
0.5943 Remote Similarity NPD6424 Approved
0.5902 Remote Similarity NPD7652 Discontinued
0.5893 Remote Similarity NPD2700 Approved
0.5889 Remote Similarity NPD8868 Approved
0.5887 Remote Similarity NPD8041 Phase 2
0.5872 Remote Similarity NPD4825 Clinical (unspecified phase)
0.587 Remote Similarity NPD2220 Clinical (unspecified phase)
0.5833 Remote Similarity NPD1456 Approved
0.5833 Remote Similarity NPD1784 Approved
0.5784 Remote Similarity NPD5791 Phase 2
0.5743 Remote Similarity NPD9577 Approved
0.5714 Remote Similarity NPD4815 Discontinued
0.5702 Remote Similarity NPD1385 Discontinued
0.5699 Remote Similarity NPD1439 Clinical (unspecified phase)
0.5688 Remote Similarity NPD6428 Approved
0.5682 Remote Similarity NPD3192 Approved
0.5682 Remote Similarity NPD3193 Approved
0.567 Remote Similarity NPD9199 Approved
0.566 Remote Similarity NPD6432 Approved
0.566 Remote Similarity NPD6431 Approved
0.566 Remote Similarity NPD6433 Approved
0.566 Remote Similarity NPD6434 Clinical (unspecified phase)
0.5638 Remote Similarity NPD5386 Phase 2
0.5612 Remote Similarity NPD4278 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