Table 3.

2: List of selected ligands present in the 2BLE and 2C6Q at the binding sites of
either GMP or NDP or alternatives with its binding free energies.

PDB ID:2BLE

Ligand ID GMP Binding sites NDP Alternative Binding

(GMP) bindin Binding sites free
g sites energies
(kcal/mol)
Guanosine-5'-Monophosphate Yes No No -9.30
(DB01972) (N158,A287,S288,G179,V185,
S184,G221,G243,G242,M244)
Guanosine-3'-Monophosphate Yes No No -9.10
(DB03315) (N158,G179,A287,S288,G220,
G221,S184,C222,G242,G243)
2'-Deoxyguanosine-5'- Yes No No -9.30
Monophosphate (M269,S270,R286,G290,A287,
(DB04457) S184,G221,C222,G220,D219,
G243,G242)
Inosinic Acid Yes No No -8.70
(DB04566) (N158,S288,S270,G290,M269,
V185,S184,G243,G242,D219)
Cytidine-5'-Monophosphate Yes No No -9.20
( DB03403) (G179,R286,A287,D219,C222,
G221,S184,V185,M244,G242,
G243)
Guanosine-5'-Diphosphate Yes No No -8.70
(DB04315) (A287,S288,G179,G221,V185,
S184,G242,G243,M244)
N7-Methyl-Guanosine-5'- Yes No No -9.30
Monophosphate (R286,M269,S270,A287,G242,
(DB03593) S288,G243,V185,G290,S184,
G221,D219)
ADENOSINE PHOSPHATE Yes No No -9.30
(CHEMBL 752) (M269,R286,N158,G181,G220
,S184,D219,G242)
C10H13N4O7P (CHEMBL 96862) Yes No No -9.00
(N158,M269,G179,A287,S288
,G183,G221,S184,G242,G243)
C18H21ClN5O9P No No Yes -8.90
 (CHEMBL2046905) (L327,S328,
H210,R34,H
215,K213)
C9H13N2O9P (CHEMBL460901) Yes No No -8.60
(M269,R286,G179,G181,G183
,G221,S184,G243,G242
C9H14N3O8P (CHEMBL582887) Yes No No -8.40
(R286,M269,S270A287,N158,
S288,G290,V185,S184)
C18H21FN5O9P No No Yes -8.80
(CHEMBL2046907) T37,F36,H21
5,K213,H210
,F232,S328,L
324

C10H15N2O10P Yes No No -8.90

(CHEMBL3274191) (M269,R286,N158,D219,S184,
G243,G242)
Yes No No -9.10
O2'-METHYLGUANOSINE-5'-
MONOPHOSPHATE (N158,S288,G179,G242,G243,
M244,S184,C222,G221)
(OMG)
Yes No No -9.70
GUANINE ARABINOSE-5'-
PHOSPHATE (D219,V185,G179,C186,G181,
G183,S184,G221,C222,M244,
G243,G242)
(GAO)
Yes No No -9.70
3'-deoxy-guanosine 5'-
monophosphate (K177,M240,G242,G243,G221
,S184,V185,S288,A287,R286)
(GDO)
No No Yes -9.60
L-GUANOSINE-5'-
MONOPHOSPHATE G290,S270,S
288,A287,M
(LG)
269,S184,G2
43,G242,G22
1,D219,N158
Yes No No -9.50
L-GUANOSINE-5'-
MONOPHOSPHATE (M269,A287,S288,V185,D219
,S184,G220,G221,C222,M244,
(0G)
G243,G242)
 Yes No No -9.60
1N-METHYLGUANOSINE-5'-
MONOPHOSPHATE (N158,R286,S288,G179,V185,
S184,G221,C222,M244,G243,
(1MG)
G220,G242)
Yes No No -10.00
GUANOSINE-5'-PHOSPHATE
(K177,D219,R286,A287,S288,
(CPG) S184,G221,G243,G242)
Yes No No -10.00
GUANOSINE-5'-
MONOPHOSPHATE (K177,R286,A287,S288,S184,
G221,G243,G242,D219)
(G)
2'-Deoxyguanosine-5'- Yes No No -10.10
monophosphoric acid disodium salt (G179,G181,G183,S184,G221,
(ZINC_3869846) G243,M244,C222,G242,G220,
D219,M240)
Disodium 5'-Inosinate Yes No No -10.00
(ZINC_4228242) (R286,S288,K177,D219,G242,
G243,G221,S184)
[3,4-dihydroxy-5-(6-hydroxypurin-9- Yes No No -9.70
yl)-tetrahydrofuran-2- (M269,S270,S288,G290,G242,
yl]methoxyphosphonic G243,M244,G220,C222,G221,
(ZINC_8613164) S184)
[(2R,3S,4R,5R)-3,4-dihydroxy-5-(6- Yes No No -10.00
hydroxypurin-9-yl)tetrahydrofuran- K177,R286,A287,S288,D219,
2-yl]methyl G242,G243,G221,S184
(ZINC_13526981)
Ara-HxMP Yes No No -9.70
(ZINC_13531931) (M269,S270,S288,G290,G242,
G243,M244,G221,S184)
[(2R,3R,4R,5R)-3,4-dihydroxy-5-(6- Yes No No -9.90
oxo-3H-purin-9-yl)tetrahydrofuran- (S288,S270,M269,G290,G220,
2-yl]methyl G221,C222,S184,G242,G243,
(ZINC_14951277) M244)
[(2R,3S,5R)-5-(5-fluoro-4-oxo-2- Yes No No -9.30
thioxo-pyrimidin-1-yl)-3-hydroxy- (M269,S270,R286,A287,G181,
tetrahydrofuran-2-yl]methyl G179,G220,D219,G242)
(zinc_33753574)
2-amino-9-[(2S,3S,4R,5S)-3- Yes No No -8.60
hydroxy-4-methoxy-5-methylol- (A287,S288,V185,S184,D219)
tetrahydrofuran-2-yl]hypoxanthine
 (zinc_2522481)
2-amino-9-[3-hydroxy-5- Yes No No -8.40
(hydroxymethyl)-4-methoxy- (M269,S270,S271,G290,S288,
tetrahydrofuran-2-yl]-3H-purin-6- A287,G181,G183,R286)
one
(zinc_4963099)
2-amino-9-[3-hydroxy-5- Yes No No -8.40
(hydroxymethyl)-4-methoxy- (M269,S270,A287,S288,G290,
tetrahydrofuran-2-yl]-3H-purin-6- V185,C186,G242,G220,M240)
one
(zinc_4963101)
2'-O-Methylguanosine Yes No No -8.90
(zinc_5998211) (K177,N54,R286,M269,S270,
A287,S288,G290,S184)
2'-O-Methylguanosine Yes No No -8.70
(zinc_8830753) (M269,R286,S270,A287,S288,
G290,G181,G183,G179,D219)
2'-O-Methylguanosine Yes No No -9.30
(zinc_8830754) (M269,R286,S270,A287,S288,
G290,G181,G183)
2'-O-Methylguanosine Yes No No -8.50
(zinc_8830755) (D219,G179R286,A287,S288,
V185,S184,G183)

2'-O-Methylguanosine Yes No No -9.40

(zinc_13783929) (R286,A287,S288,G290,S270,
M269,G181,G183)
2-amino-9-[(2S,3S,4S,5S)-3- Yes No No -8.90
hydroxy-5-(hydroxymethyl)-4- (M269,R286,A287,S288,V185,
methoxy-tetrahydrofuran-2-yl]-1H- G179,D219,N158)
purin-6-one
(zinc_83290877)
PDB ID: 2C6Q

Ligand ID GMP NDP Alternative Binding Binding

(GMP) Binding bindi sites free
sites ng energies
sites (kcal/mo
l)
ADENOSINE PHOSPHATE No No Yes -7.50
(CHEMBL752) 7 (H210,H215,S37,D237,
R34,K325,S328)

C9H13N2O9P No No Yes -6.90

(CHEMBL460901) (S328,R329,R34,G214,
H210,G325)
C9H14N3O8P No No Yes -6.90
(CHEMBL582887) (H210,G235,S328,R32
9,K325,R34,D237)
C10H13N4O7P No No Yes -7.10
(CHEMBL96862) (H210,H215,S37,G235,
S328,R34,S35)
C18H21ClN5O9P No No Yes -8.30
(CHEMBL2046905) (G214,H215,S37,H210,
D237,R34,K325,R329,
S328)
C18H21FN5O9P No No Yes -8.20
(CHEMBL2046907) (K213,H215,S37,H210,
A236,S328,R329,K325,
R34)
C10H15N2O10P No No Yes -7.20
(CHEMBL3274191) (H210,S37,R34,S328,G
325)
Guanosine-5'-Monophosphate No No Yes -7.60
(DB01972) (G106,S108,D109,L78,
N54,M269,D129)
Guanosine-3'-Monophosphate No No Yes -7.20
(DB03315) (K277,D56,H77,T80,E6
2,S249,K264)
 Cytidine-5'-Monophosphate No No Yes -7.00
(DB03403) (D207,A206,H210,R34,
S328,T331,F333)
Guanosine-5'-Diphosphate No No Yes -7.70
(DB04315) (G253,D56,K277,Y278,
H77,Y80,Q84,E62,F61,
F88,N92)
2'-Deoxyguanosine-5'- No No Yes -7.30
Monophosphate (H79,Y80,H77,T60,E62
(DB04457) ,E250,D56,Y278,K277,
Y267,G253,K264,L255
)
Inosinic Acid No No Yes -7.10
(DB04566) (S249,K264,G253,E254
,K277,Y80,H77)
N7-Methyl-Guanosine-5'- No No Yes -7.30
Monophosphate (G106,D109,S108,K78,
( DB03593) N54)
No No Yes -8.10
GUANOSINE-5'-PHOSPHATE
(S328,A236,H210,R34,
(CPG) S35,F36,S37)
No No Yes -8.00
3'-deoxy-guanosine 5'-
monophosphate (H210,G235,S328,S37,
F36,S35,R34)
(GDO)
No No Yes -7.40
1N-METHYLGUANOSINE-5'-
MONOPHOSPHATE (S328,H210,K213,A23
6,H215,R34,S35,S37)
(1MG)
No No Yes -7.80
GUANOSINE-5'-
MONOPHOSPHATE (H210,K213,H215,S37,
F36,S35,R34,K325,A23
(G25)
6,S328)
No No Yes -8.00
GUANINE ARABINOSE-5'-
PHOSPHATE (K213,S37,F36,S35,R3
4,A236,S328,G235,H21
(GAO)
0)
No No Yes -7.80
[(1R,3R,4R,7S)-7-HYDROXY-3-
(GUANIN-9-YL)-2,5- (H210,G214,S37,F36,R
DIOXABICYCLO[2.2.1]HEPT- 34,R329,S328)
1-YL]METHYL DIHYDROGEN
 PHOSPHATE
(LCG)
No No Yes -7.50
L-GUANOSINE-5'-
MONOPHOSPHATE (H210,H215,K213,S37,
F36,S35,R34,S328,A23
(LG)
6)
No No Yes -7.90
L-GUANOSINE-5'-
MONOPHOSPHATE (T105,G106,D109,K78)

(OG)
No No Yes -7.70
GUANOSINE-5'-
MONOPHOSPHATE (H210,H215,K213,S37,
F36,S35,R34,S328,G23
O2'-METHYLGUANOSINE-5'-
5)
MONOPHOSPHATE
(OMG)
2'-Deoxyguanosine-5'- No No Yes -7.10
monophosphoric acid disodium (D109,D129,K78,N54,
salt H79,Y278)
(ZINC_3869846)
Disodium 5'-Inosinate No No Yes -7.30
(ZINC_4228242) (S328,A236,H210,H21
5,F36,R34,S35,S37)
[3,4-dihydroxy-5-(6- No No Yes -7.50
hydroxypurin-9-yl)- (S108,D109,Q112,K78,
tetrahydrofuran-2- H79,M269,A274)
yl]methoxyphosphonic
(ZINC_8613164)
[(2R,3S,4R,5R)-3,4-dihydroxy-5- No No Yes -7.40
(6-hydroxypurin-9- (H210,H215,S37,F36,S
yl)tetrahydrofuran-2-yl]methyl 35,R34,S328)
(ZINC_13526981)
Ara-HxMP No No Yes -7.40
(ZINC_13531931) (H210,H215,S37,F36,S
35,R34,S328,G335)
[(2R,3R,4R,5R)-3,4-dihydroxy-5- No No Yes -7.40
(6-oxo-3H-purin-9- (H210,G235,,S328,R34
yl)tetrahydrofuran-2-yl]methyl ,S35,S37)
ZINC_14951277
2-amino-9-[(2S,3S,4R,5S)-3- No No Yes -6.70
hydroxy-4-methoxy-5-methylol- (R34,D237,S328,G235,
tetrahydrofuran-2- H210)
yl]hypoxanthine
 (ZINC_2522481)

2-amino-9-[3-hydroxy-5- No No Yes -6.30

(hydroxymethyl)-4-methoxy- (S328,G235,H210,D23
tetrahydrofuran-2-yl]-3H-purin-6- 7,R34)
one
(ZINC_4963099)
2-amino-9-[3-hydroxy-5- No No Yes -6.60
(hydroxymethyl)-4-methoxy- (R286,M269,H79,Q112
tetrahydrofuran-2-yl]-3H-purin-6- )
one
(ZINC_4963101)
2'-O-Methylguanosine No No Yes -6.60
(zinc_5998211) (R34,H215,H210,S328)
2'-O-Methylguanosine No No Yes -6.40
(ZINC_8830753) (H210,S37,G235,D237,
S328,R34)
2'-O-Methylguanosine No No Yes -6.80
(ZINC_8830754) (H210,D237,G235,S32
8,R34,S35)
2'-O-Methylguanosine No No Yes -6.50
(zinc_8830755) (S328,H210,G214,K21
3A236,D237,R34)
2'-O-Methylguanosine No No Yes -6.60
(ZINC_13783929) (S328,G235,H210,D23
7,R34,S37)
[(2R,3S,5R)-5-(5-fluoro-4-oxo-2- No No Yes -6.80
thioxo-pyrimidin-1-yl)-3- (H210,H215,S37,G235,
hydroxy-tetrahydrofuran-2- S328,F232,R34,S35)
yl]methyl
(zinc_33753574)
2-amino-9-[(2S,3S,4S,5S)-3- No No Yes -6.90
hydroxy-5-(hydroxymethyl)-4- (G214,H210,G235,D23
methoxy-tetrahydrofuran-2-yl]- 7,S328,R34,S35)
1H-purin-6-one
(ZINC_83290877)