NPASS Compound

Natural Product: NPC485509

Natural Product ID	NPC485509
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	KDQAABAKXDWYSZ-PNYVAJAMSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	5388983
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0002756] Vinca alkaloids

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 124131 0 0 0 0 0 0 0 0999 V2000 -3.1835 4.7353 1.5881 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1209 3.7890 0.8560 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4434 2.5754 1.7051 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.1106 1.8937 1.9841 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2796 0.4967 1.3544 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0294 -0.2738 1.3240 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0647 -1.3728 0.2696 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5976 -1.6623 -0.0413 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4291 -1.1247 0.6909 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7790 -1.4395 0.4594 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0554 -2.3244 -0.5477 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0105 -2.8726 -1.2931 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3118 -2.5632 -1.0655 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3465 -3.0968 -1.7989 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2038 -4.0047 -2.8462 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4735 -2.4764 -0.6083 N 0 0 0 0 0 0 0 0 0 0 0 0 4.1300 -3.5821 -1.2648 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0849 -1.3392 0.0956 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0533 -1.0384 1.1011 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3225 -1.9517 2.3210 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5815 -1.2186 3.3892 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9475 0.1808 3.1163 N 0 0 0 0 0 0 0 0 0 0 0 0 4.0724 0.4900 3.9188 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3785 0.5052 3.2250 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4372 0.8534 1.9528 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1937 1.2224 1.2431 C 0 0 2 0 0 0 0 0 0 0 0 0 3.7166 2.6155 1.6639 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7189 3.6970 1.4232 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0660 0.3018 1.7074 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2663 1.1584 -0.2257 C 0 0 2 0 0 0 0 0 0 0 0 0 4.4883 -0.2356 -0.7973 C 0 0 2 0 0 0 0 0 0 0 0 0 3.8444 -0.3628 -2.1238 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5566 -0.6106 -3.1221 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4809 -0.2206 -2.3296 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8478 -0.3373 -3.5899 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8766 -0.3603 -0.9964 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2944 1.9993 -0.7082 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0550 2.9907 -1.6200 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9120 3.1802 -2.0526 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1923 3.8289 -2.0761 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7939 -0.8844 -0.9262 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1207 -0.9174 -1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2074 -1.4544 -0.3004 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0788 -0.4467 0.3519 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5947 0.3960 1.3461 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.4240 -0.0886 2.0649 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3995 1.7221 0.9143 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2857 -0.3322 -2.4481 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4405 -0.1052 -3.2081 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3400 0.4927 -4.4538 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1169 0.8668 -4.9543 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0017 0.6322 -4.1876 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0644 0.0329 -2.9301 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1888 -0.3082 -2.0003 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.5072 -2.6465 0.8423 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6563 -2.7335 2.0849 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7864 -3.8073 0.1398 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2004 -4.9509 0.8504 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0152 3.0668 2.8776 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3917 -0.4206 0.1093 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2634 -0.4756 0.0010 S 0 0 0 0 0 0 0 0 0 0 0 0 -0.6928 -1.4138 -1.1004 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8158 -0.9270 1.3417 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9533 1.0164 -0.3108 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2701 4.9596 1.0086 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9585 4.2742 2.5702 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7409 5.6843 1.8208 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5897 3.4923 -0.0777 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0377 4.3167 0.5324 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2509 2.3844 1.5357 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0205 1.7860 3.0787 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5185 0.7692 0.2768 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7631 -0.6619 2.3246 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2077 0.4684 1.0288 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2885 -0.4393 1.5061 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2367 -3.5740 -2.0889 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5100 -4.8117 -2.5134 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1927 -4.5105 -2.9940 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8892 -3.5403 -3.7993 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8722 -4.5200 -0.6979 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2356 -3.4986 -1.2169 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7745 -3.7441 -2.3027 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9818 -1.8066 0.6038 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8229 -2.9241 2.0497 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3892 -2.0790 2.4914 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5113 -1.3779 3.3072 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9951 -1.5170 4.3889 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9430 1.4044 4.5692 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1902 -0.3244 4.7122 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3132 0.2290 3.7544 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4124 0.8663 1.4325 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2765 2.6190 2.6826 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8212 2.8966 1.0130 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3884 4.4839 0.7023 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8556 4.1979 2.4440 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6939 3.2532 1.1695 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1264 0.8280 1.3548 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2747 1.4704 -0.6633 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6813 -1.4211 -3.7709 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4190 0.1066 -4.4200 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8637 0.1773 -3.5428 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3133 -0.8354 -0.2508 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0114 4.0965 -3.1269 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3117 4.6946 -1.3952 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1649 3.2662 -2.0086 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9024 -2.0219 -1.0040 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8726 -2.2571 0.3703 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0351 -0.9158 0.7422 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4798 0.1980 -0.4954 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4749 -1.1366 2.2823 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5576 0.3885 3.0999 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1317 1.8440 -0.1658 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3885 2.2471 0.9932 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3995 -0.4028 -2.8092 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2136 0.6759 -5.0539 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0476 1.3415 -5.9460 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0405 0.9156 -4.5584 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1571 -0.1400 -2.1071 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4970 -5.0484 1.7195 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2109 -4.7927 1.3119 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1933 -5.8656 0.2217 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9675 3.2516 2.7364 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7908 0.4505 -0.1003 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4572 1.7702 0.0595 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 1 0 11 16 1 0 16 17 1 0 16 18 1 0 18 19 1 0 19 20 1 1 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 2 0 25 26 1 0 26 27 1 6 27 28 1 0 26 29 1 0 26 30 1 0 30 31 1 0 31 32 1 0 32 33 2 0 32 34 1 0 34 35 1 0 31 36 1 6 30 37 1 0 37 38 1 0 38 39 2 0 38 40 1 0 7 41 1 0 41 42 2 0 42 43 1 0 43 44 1 0 44 45 1 0 45 46 1 0 45 47 1 0 42 48 1 0 48 49 2 0 49 50 1 0 50 51 2 0 51 52 1 0 52 53 2 0 53 54 1 0 7 55 1 1 55 56 2 0 55 57 1 0 57 58 1 0 3 59 1 1 60 61 1 0 61 62 2 0 61 63 2 0 61 64 1 0 47 3 1 0 53 48 1 0 46 5 1 0 13 8 1 0 31 18 1 0 54 41 1 0 19 10 1 0 29 22 1 0 29 19 1 0 1 65 1 0 1 66 1 0 1 67 1 0 2 68 1 0 2 69 1 0 4 70 1 0 4 71 1 0 5 72 1 6 6 73 1 0 6 74 1 0 9 75 1 0 12 76 1 0 15 77 1 0 15 78 1 0 15 79 1 0 17 80 1 0 17 81 1 0 17 82 1 0 18 83 1 1 20 84 1 0 20 85 1 0 21 86 1 0 21 87 1 0 23 88 1 0 23 89 1 0 24 90 1 0 25 91 1 0 27 92 1 0 27 93 1 0 28 94 1 0 28 95 1 0 28 96 1 0 29 97 1 6 30 98 1 6 35 99 1 0 35100 1 0 35101 1 0 36102 1 0 40103 1 0 40104 1 0 40105 1 0 43106 1 0 43107 1 0 44108 1 0 44109 1 0 46110 1 0 46111 1 0 47112 1 0 47113 1 0 49114 1 0 50115 1 0 51116 1 0 52117 1 0 54118 1 0 58119 1 0 58120 1 0 58121 1 0 59122 1 0 60123 1 0 64124 1 0 M END

Standard InCHIKey	KDQAABAKXDWYSZ-PNYVAJAMSA-N
Standard InCHI	InChI=1S/C46H58N4O9.H2O4S/c1-8-42(54)23-28-24-45(40(52)57-6,36-30(15-19-49(25-28)26-42)29-13-10-11-14-33(29)47-36)32-21-31-34(22-35(32)56-5)48(4)38-44(31)17-20-50-18-12-16-43(9-2,37(44)50)39(59-27(3)51)46(38,55)41(53)58-7;1-5(2,3)4/h10-14,16,21-22,28,37-39,47,54-55H,8-9,15,17-20,23-26H2,1-7H3;(H2,1,2,3,4)/t28-,37-,38+,39+,42-,43+,44+,45-,46-;/m0./s1
SMILES	CC[C@@]1(C[C@H]2C[C@](c3cc4c(cc3OC)N(C)[C@@H]3[C@@]54CCN4CC=C[C@](CC)([C@@H]54)[C@H]([C@@]3(C(=O)OC)O)OC(=O)C)(c3c(CCN(C2)C1)c1ccccc1[nH]3)C(=O)OC)O.OS(=O)(=O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	810.42	Volume:	821.262 ? Van der Waals volume.
Dense:	0.987	LogP:	3.014 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.836 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.282 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	10.0	Rigid Bonds:	48.0
TPSA:	154.1 ? Topological Polar Surface Area.	H-Bond Acceptor:	13.0
H-Bond Donor:	3.0	Rings:	9.0
Heavy Atoms:	13.0

MedChem Properties

QED Drug-Likeness Score:	0.18	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.152	Fsp³:	0.587
MCE-18:	269.589 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.261	Fluc inhibitor:	0.002 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.872 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.714 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.001	Promiscuous compounds:	0.989

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.451	MDCK Permeability:	-5.345
Pgp-inhibitor:	0.0	Pgp-substrate:	1.0
PAMPA:	0.367 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.0
20% Bioavailability (F20%):	0.033	30% Bioavailability (F30%):	0.952
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.006	MRP1:	1.0
Plasma Protein Binding (PPB):	73.977%	Volume Distribution (VD):	0.428
Fu:	25.692% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.978
OATP1B3 inhibitor:	0.998	BCRP inhibitor:	0.64
BSEP inhibitor:	0.975

ADMET: Metabolism

CYP1A2-inhibitor:	0.999	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	1.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.013
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	1.0
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	0.847
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.2
HLM stability:	0.977 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

6.028

Half-life (T1/2):

1.743

ADMET: Toxicity

hERG Blockers:	0.832	hERG Blockers (10um):	0.257
Human Hepatotoxicity (H-HT):	0.929	Drug-induced Liver Injury (DILI):	0.896
AMES Toxicity:	0.775	Rat Oral Acute Toxicity:	0.925
Maximum Recommended Daily Dose:	1.0	Skin Sensitization:	1.0
Carcinogencity:	0.243	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.999
Drug-induced Neurotoxicity:	0.965	Ototoxicity:	0.942
Hematotoxicity:	0.797	Drug-induced Nephrotoxicity:	1.0
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.68
A549 Cytotoxicity:	0.999	Hek293 Cytotoxicity:	0.983
BCF:	0.646 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	3.879 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.593 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.888 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO15289	Scoparia dulcis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12880314]
NPO15289	Scoparia dulcis	Species	Plantaginaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[1294695]
NPO15289	Scoparia dulcis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15104516]
NPO15289	Scoparia dulcis	Species	Plantaginaceae	Eukaryota	leaves and twigs	Taiwan	n.a.	PMID[1659612]
NPO15289	Scoparia dulcis	Species	Plantaginaceae	Eukaryota	aerial parts	Nanning, Guangxi Zhuang Autonomous Region, Peoples Republic of China	2012-OCT	PMID[24955889]
NPO15289	Scoparia dulcis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15289	Scoparia dulcis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15289	Scoparia dulcis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15289	Scoparia dulcis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15289	Scoparia dulcis	Species	Plantaginaceae	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	Organism Name	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

Activity Type	# Activity
IC50	60
Inhibition	9
EC50	3
Activity	13
ED50	6
TGI	7
IC50 relative	1

Activity Type	# Activity
Cell line	54
Protein family	7
Protein complex	1
Individual protein	4
Organism	17
Single protein	1
Non-molecular	13
Others	2

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT67	Individual protein	Cholinesterase	Equus caballus	Inhibition	=	0.36	%	PMID[23062825]
NPT20556	Single protein	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	-11.69	%	DOI[10.6019/CHEMBL4495564]
NPT692	Individual protein	Histone deacetylase 6	Homo sapiens	Inhibition	=	-5.21	%	HDAC6 screening dataset using tau-based substrate in an enzymatic assay yields selective inhibitors and activators
NPT692	Individual protein	Histone deacetylase 6	Homo sapiens	Inhibition	=	-11.33	%	HDAC6 screening dataset using tau-based substrate in an enzymatic assay yields selective inhibitors and activators
NPT3014	Protein family	Tubulin	Sus scrofa	IC50	=	130.0	nM	PMID[12852768]
NPT3014	Protein family	Tubulin	Sus scrofa	IC50	=	130.0	nM	PMID[17181164]
NPT3014	Protein family	Tubulin	Sus scrofa	IC50	=	130.0	nM	PMID[17973361]
NPT3014	Protein family	Tubulin	Sus scrofa	IC50	=	130.0	nM	PMID[19220018]
NPT3014	Protein family	Tubulin	Sus scrofa	IC50	=	130.0	nM	PMID[20537765]
NPT518	Protein complex	Tubulin	Homo sapiens	IC50	=	130.0	nM	PMID[20546980]
NPT3014	Protein family	Tubulin	Sus scrofa	IC50	=	130.0	nM	PMID[21563750]
NPT3014	Protein family	Tubulin	Sus scrofa	IC50	=	130.0	nM	PMID[21705223]
NPT66	Individual protein	Acetylcholinesterase	Electrophorus electricus	Inhibition	=	15.44	%	PMID[23062825]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT111	Cell line	K562	Homo sapiens	IC50	=	1.0	nM	PMID[12852768]
NPT858	Cell line	LNCaP	Homo sapiens	EC50	=	500.0	nM	PMID[12361397]
NPT2641	Cell line	COLO 320	Homo sapiens	EC50	<	80.0	nM	PMID[12361397]
NPT396	Cell line	T47D	Homo sapiens	EC50	<	80.0	nM	PMID[12361397]
NPT517	Cell line	Panel NCI-60 (60 carcinoma cell lines)	Homo sapiens	Activity	=	25.0	pM	PMID[16750365]
NPT111	Cell line	K562	Homo sapiens	IC50	=	1.0	nM	PMID[17181164]
NPT111	Cell line	K562	Homo sapiens	IC50	=	1.0	nM	PMID[17973361]
NPT81	Cell line	A549	Homo sapiens	IC50	=	0.002	ug.mL-1	PMID[9214732]
NPT180	Cell line	HCT-8	Homo sapiens	IC50	=	0.005	ug.mL-1	PMID[9214732]
NPT111	Cell line	K562	Homo sapiens	IC50	=	1.0	nM	PMID[19220018]
NPT3045	Cell line	NUGC-4	Homo sapiens	ED50	=	5.3	uM	PMID[12880314]
NPT492	Cell line	Caco-2	Homo sapiens	IC50	=	69000.0	nM	PMID[19467877]
NPT2287	Cell line	COR-L23	Homo sapiens	IC50	=	45500.0	nM	PMID[19467877]
NPT81	Cell line	A549	Homo sapiens	IC50	=	67300.0	nM	PMID[19467877]
NPT858	Cell line	LNCaP	Homo sapiens	IC50	=	29300.0	nM	PMID[19467877]
NPT2282	Cell line	C32	Homo sapiens	IC50	=	3000.0	nM	PMID[19467877]
NPT1083	Cell line	A-375	Homo sapiens	IC50	=	7200.0	nM	PMID[19467877]
NPT369	Cell line	ACHN	Homo sapiens	IC50	=	22700.0	nM	PMID[19467877]
NPT111	Cell line	K562	Homo sapiens	IC50	=	1.0	nM	PMID[20537765]
NPT111	Cell line	K562	Homo sapiens	IC50	=	1.0	nM	PMID[20546980]
NPT111	Cell line	K562	Homo sapiens	IC50	=	1.0	nM	PMID[21563750]
NPT111	Cell line	K562	Homo sapiens	IC50	=	1.0	nM	PMID[21705223]
NPT139	Cell line	HT-29	Homo sapiens	IC50	=	550.0	nM	PMID[21920762]
NPT2644	Cell line	UACC-903	Homo sapiens	IC50	=	1650.0	nM	PMID[21920762]
NPT81	Cell line	A549	Homo sapiens	IC50	=	2360.0	nM	PMID[22546674]
NPT90	Cell line	DU-145	Homo sapiens	IC50	=	4250.0	nM	PMID[22546674]
NPT373	Cell line	SK-MEL-5	Homo sapiens	IC50	=	1740.0	nM	PMID[22546674]
NPT1081	Cell line	BXPC-3	Homo sapiens	IC50	=	1130.0	nM	PMID[22546674]
NPT65	Cell line	HepG2	Homo sapiens	IC50	=	160.0	nM	PMID[22546674]
NPT139	Cell line	HT-29	Homo sapiens	IC50	=	11180.0	nM	PMID[22546674]
NPT83	Cell line	MCF7	Homo sapiens	IC50	=	24080.0	nM	PMID[22546674]
NPT82	Cell line	MDA-MB-231	Homo sapiens	IC50	=	31520.0	nM	PMID[22546674]
NPT65	Cell line	HepG2	Homo sapiens	IC50	=	56.0	nM	PMID[23708010]
NPT111	Cell line	K562	Homo sapiens	IC50	=	16.0	nM	PMID[23708010]
NPT65	Cell line	HepG2	Homo sapiens	IC50	=	19.0	nM	PMID[23708010]
NPT83	Cell line	MCF7	Homo sapiens	IC50	=	7.0	nM	PMID[23708010]
NPT82	Cell line	MDA-MB-231	Homo sapiens	IC50	=	8.3	nM	PMID[23708010]
NPT2831	Cell line	P388/S	Mus musculus	Activity	=	92.0	%	PMID[430477]
NPT2831	Cell line	P388/S	Mus musculus	Activity	=	96.0	%	PMID[430477]
NPT2831	Cell line	P388/S	Mus musculus	Activity	=	75.0	%	PMID[430477]
NPT5929	Cell line	P388/VCR	Mus musculus	Activity	=	17.0	%	PMID[430477]
NPT5929	Cell line	P388/VCR	Mus musculus	Activity	=	12.0	%	PMID[430477]
NPT5929	Cell line	P388/VCR	Mus musculus	Activity	=	10.0	%	PMID[430477]
NPT5929	Cell line	P388/VCR	Mus musculus	Activity	=	9.0	%	PMID[430477]
NPT1161	Cell line	CHO	Cricetulus griseus	Activity	=	40.0	%	PMID[430477]
NPT1161	Cell line	CHO	Cricetulus griseus	Activity	=	15.0	%	PMID[430477]
NPT1161	Cell line	CHO	Cricetulus griseus	Activity	=	3.0	%	PMID[430477]
NPT1629	Cell line	CWR22R	Homo sapiens	IC50	=	1.0	nM	PMID[38237151]
NPT393	Cell line	HCT-116	Homo sapiens	IC50	=	1.0	nM	PMID[38237151]
NPT65	Cell line	HepG2	Homo sapiens	IC50 relative	=	4000.0	nM	ECBD screening data for assay EOS300108
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	0.52	nM	PMID[19734910]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	1.05	nM	PMID[19734910]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	0.93	nM	PMID[19734910]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	1.0	nM	PMID[19734910]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	0.32	nM	PMID[19734910]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	398.11	nM	PMID[19734910]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	1000.0	nM	PMID[19734910]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	5011.87	nM	PMID[19734910]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	2511.89	nM	PMID[19734910]
NPT20555	Organism	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	33.96	%	DOI[10.21203/rs.3.rs-23951/v1]
NPT20555	Organism	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	2.76	%	DOI[10.6019/CHEMBL4495565]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	ED50	=	5.9	uM	PMID[12880314]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	ED50	=	6.1	uM	PMID[12880314]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	ED50	=	5.3	uM	PMID[12880314]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	=	45600.0	nM	PMID[19467877]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	TGI	=	76.0	%	PMID[430477]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	TGI	=	0.0	%	PMID[430477]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	TGI	=	51.0	%	PMID[430477]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	TGI	<	25.0	%	PMID[412968]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	TGI	=	54.0	%	PMID[412968]
NPT27	Others	Unspecified	n.a.	IC50	=	37600.0	nM	PMID[19467877]
NPT2	Others	Unspecified	n.a.	Inhibition	=	66.0	%	PMID[21920762]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference
-	Rattus norvegicus	LD50	=	2.9	mg.kg-1	PMID[412968]
-	Mus musculus	LD50	=	10.0	mg.kg-1	PMID[412968]
-	Mus musculus	LD50	=	10.0	mg.kg-1	PMID[430477]

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC485509 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	20143
0.1-0.2	29007
0.2-0.3	675
0.3-0.4	23
0.4-0.5	1
0.5-0.6	1
0.6-0.7	2
0.7-0.8	2
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
0.9667	High Similarity	NPC195788
0.9667	High Similarity	NPC237901
0.8015	Intermediate Similarity	NPC608514
0.7939	Intermediate Similarity	NPC277353
0.7939	Intermediate Similarity	NPC600057
0.7183	Intermediate Similarity	NPC489610
0.6901	Remote Similarity	NPC260909
0.6786	Remote Similarity	NPC302688
0.5762	Remote Similarity	NPC481036

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC485509 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3923
0.1-0.2	5142
0.2-0.3	69
0.3-0.4	2
0.4-0.5	0
0.5-0.6	0
0.6-0.7	6
0.7-0.8	2
0.8-0.85	2
0.85-0.9	1
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD8465	Approved
0.9667	High Similarity	NPD8466	Phase 4
0.9667	High Similarity	NPD8467	Approved
0.8583	High Similarity	NPD8489	Phase 1
0.8244	Intermediate Similarity	NPD8363	Approved
0.8015	Intermediate Similarity	NPD8364	Approved
0.7836	Intermediate Similarity	NPD8365	Clinical (unspecified phase)
0.7183	Intermediate Similarity	NPD8459	Approved
0.6944	Remote Similarity	NPD8427	Approved
0.6901	Remote Similarity	NPD8460	Phase 4
0.6857	Remote Similarity	NPD8425	Approved
0.6857	Remote Similarity	NPD8426	Phase 4
0.6786	Remote Similarity	NPD8428	Approved
0.6786	Remote Similarity	NPD8429	Phase 4

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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