Receptor
PDB id Resolution Class Description Source Keywords
1ZNX 2.35 Å EC: 2.7.4.8 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS GUANYLATE KI COMPLEX WITH GMP MYCOBACTERIUM TUBERCULOSIS GUANYLATE KINASE GMP KINASE ATP:GMP-PHOSPHOTRANSFERASE TR
Ref.: UNIQUE GMP-BINDING SITE IN MYCOBACTERIUM TUBERCULOS GUANOSINE MONOPHOSPHATE KINASE PROTEINS V. 62 489 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5GP A:300;
Valid;
none;
submit data
363.221 C10 H14 N5 O8 P c1nc2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1ZNY 2.3 Å EC: 2.7.4.8 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS GUANYLATE KI COMPLEX WITH GDP MYCOBACTERIUM TUBERCULOSIS GUANYLATE KINASE GMP KINASE ATP:GMP-PHOSPHOTRANSFERASE TR
Ref.: UNIQUE GMP-BINDING SITE IN MYCOBACTERIUM TUBERCULOS GUANOSINE MONOPHOSPHATE KINASE PROTEINS V. 62 489 2006
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1ZNY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 1ZNX - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
3 1ZNZ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1ZNY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 1ZNX - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
3 1ZNZ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1EX7 - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
2 1GKY - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
3 2F3R ic50 = 0.5 uM G5P C20 H29 N10 O23 P5 c1nc(c2c(n....
4 2AN9 - GMP C10 H13 N5 O5 c1nc2c(n1[....
5 1LVG - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
6 1ZNY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 1ZNX - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
8 1ZNZ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 4QRH Ki = 7 uM 0O2 C10 H18 N5 O20 P5 c1nc2c(n1[....
10 2J41 - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5GP; Similar ligands found: 156
No: Ligand ECFP6 Tc MDL keys Tc
1 5GP 1 1
2 G 1 1
3 GDP 0.828947 0.986486
4 GP3 0.815789 0.960526
5 GP2 0.805195 0.948052
6 GTP 0.797468 0.986486
7 GNH 0.794872 0.973333
8 G2P 0.777778 0.948052
9 GMV 0.775 0.960526
10 GCP 0.765432 0.960526
11 G1R 0.765432 0.973333
12 GDP MG 0.7625 0.935065
13 GAV 0.759036 0.948052
14 GSP 0.756098 0.935897
15 GNP 0.756098 0.960526
16 GDP BEF 0.753086 0.911392
17 ALF 5GP 0.753086 0.9
18 GMP 0.732394 0.866667
19 GTP MG 0.72619 0.935065
20 BEF GDP 0.72619 0.9
21 GPG 0.724138 0.948052
22 GCP G 0.717647 0.947368
23 G2R 0.712644 0.948052
24 GDP AF3 0.701149 0.9
25 GDP ALF 0.701149 0.9
26 Y9Z 0.692308 0.890244
27 GDC 0.692308 0.948052
28 GKE 0.692308 0.948052
29 GDD 0.692308 0.948052
30 YGP 0.681319 0.9125
31 G G 0.677778 0.947368
32 G3A 0.677419 0.960526
33 G5P 0.670213 0.960526
34 GFB 0.666667 0.948052
35 GDR 0.666667 0.948052
36 GTG 0.666667 0.924051
37 6CK 0.659574 0.924051
38 3GP 0.65 0.959459
39 GKD 0.645833 0.948052
40 JB2 0.645833 0.948052
41 GPD 0.639175 0.9125
42 GDX 0.639175 0.960526
43 GDP 7MG 0.635417 0.923077
44 G3D 0.617977 0.972973
45 U2G 0.617647 0.924051
46 IMP 0.609756 0.972603
47 2GP 0.609756 0.946667
48 JB3 0.607843 0.935897
49 CG2 0.605769 0.924051
50 G4P 0.604396 0.972973
51 DGP 0.60241 0.922078
52 DG 0.60241 0.922078
53 FEG 0.601942 0.890244
54 NGD 0.601942 0.948052
55 ZGP 0.596154 0.879518
56 0O2 0.595745 0.972973
57 2MD 0.584906 0.879518
58 G7M 0.583333 0.960526
59 CAG 0.583333 0.869048
60 G A A A 0.579439 0.935065
61 U A G G 0.574074 0.947368
62 MGD 0.568807 0.879518
63 DBG 0.566372 0.935897
64 PGD 0.5625 0.9125
65 MD1 0.5625 0.879518
66 P2G 0.55814 0.894737
67 FE9 0.553571 0.784946
68 I2C FE2 CMO CMO 0.54955 0.818182
69 P1G 0.545455 0.883117
70 GH3 0.542553 0.96
71 TPG 0.53913 0.829545
72 GPX 0.53125 0.933333
73 DGI 0.527473 0.910256
74 G1R G1R 0.525862 0.911392
75 PGD O 0.521368 0.83908
76 DGT 0.521277 0.910256
77 G4M 0.520325 0.869048
78 G G U 0.519231 0.947368
79 G C 0.513514 0.911392
80 93A 0.511364 0.821429
81 IDP 0.505495 0.959459
82 MGQ 0.505155 0.948052
83 C2R 0.5 0.893333
84 BGO 0.5 0.911392
85 AMP 0.5 0.905405
86 AMZ 0.5 0.905405
87 A 0.5 0.905405
88 AIR 0.493671 0.890411
89 MGV 0.49 0.901235
90 SGP 0.488889 0.8375
91 U G A 0.488189 0.9
92 NIA 0.488095 0.8375
93 GPC 0.474138 0.890244
94 G G G RPC 0.473684 0.886076
95 GGM 0.473684 0.888889
96 71V 0.47191 0.85
97 APC G U 0.470085 0.897436
98 MGP 0.46875 0.948052
99 C2E 0.468085 0.933333
100 35G 0.468085 0.945946
101 PCG 0.468085 0.945946
102 G1G 0.466102 0.9125
103 7RA 0.465909 0.918919
104 AAM 0.465909 0.905405
105 RMB 0.465909 0.813333
106 FAI 0.465909 0.905405
107 1RB 0.465116 0.824324
108 6G0 0.463918 0.948052
109 5GP 5GP 0.463158 0.894737
110 G G G C 0.462185 0.924051
111 RBZ 0.45977 0.815789
112 UCG 0.459016 0.923077
113 A G C C 0.458333 0.923077
114 DG DG 0.456311 0.876543
115 G U34 0.45614 0.9
116 IMO 0.449438 0.866667
117 A G U 0.446154 0.9
118 G C C C 0.443548 0.935897
119 IRN 0.443038 0.808219
120 PMO 0.43956 0.792208
121 7RP 0.438202 0.864865
122 GTA 0.436364 0.924051
123 P2P 0.433333 0.842105
124 JLN 0.433333 0.88
125 XMP 0.428571 0.907895
126 PGS 0.425532 0.804878
127 RVP 0.423529 0.84
128 G2Q 0.423077 0.948052
129 ADP 0.419355 0.906667
130 A2D 0.417582 0.881579
131 ABM 0.417582 0.857143
132 GUO 0.415842 0.932432
133 CA0 0.410526 0.883117
134 2SA 0.41 0.871795
135 1YD 0.409091 0.933333
136 4BW 0.409091 0.933333
137 AP2 0.408602 0.871795
138 A12 0.408602 0.871795
139 BA3 0.408602 0.881579
140 6C6 0.408163 0.825
141 25A 0.407767 0.906667
142 NOS 0.406977 0.813333
143 AMP MG 0.406593 0.833333
144 ATP 0.40625 0.906667
145 AP5 0.404255 0.881579
146 B4P 0.404255 0.881579
147 6IA 0.40404 0.785714
148 ACQ 0.40404 0.883117
149 ANP 0.40404 0.883117
150 CGP 0.403361 0.878049
151 3ZE 0.402062 0.871795
152 APC 0.402062 0.871795
153 5FA 0.402062 0.906667
154 AQP 0.402062 0.906667
155 N6P 0.4 0.853333
156 AN2 0.4 0.894737
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1ZNY; Ligand: GDP; Similar sites found: 63
This union binding pocket(no: 1) in the query (biounit: 1zny.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4IAW LIZ 0.001094 0.43308 None
2 5NCF 8T5 0.008883 0.40751 None
3 3MTX PGT 0.04407 0.40275 1.3245
4 3MBG FAD 0.0305 0.40523 1.43885
5 5MW8 ATP 0.02285 0.4075 1.44928
6 3QXV MTX 0.005686 0.43141 1.5873
7 3JU6 ANP 0.005377 0.41811 1.93237
8 4YVN EBS 0.0007233 0.46346 2.41546
9 5H9Y BGC BGC BGC BGC 0.001389 0.4577 2.41546
10 3CBC DBS 0.004282 0.42847 2.52525
11 3WV6 GAL GLC 0.00289 0.40815 2.89855
12 3WV6 GAL BGC 0.008737 0.40371 2.89855
13 1LSH PLD 0.009226 0.43674 3.38164
14 4WOE ADP 0.00547 0.42032 3.38164
15 4NOS ITU 0.00743 0.40362 3.38164
16 5UIU 8CG 0.0493 0.4001 3.38164
17 4QYN RTL 0.01912 0.41153 3.7594
18 2YMZ LAT 0.002005 0.4165 3.84615
19 1WUB OTP 0.01402 0.43999 3.93258
20 2VDF OCT 0.0001038 0.54509 4.34783
21 2G30 ALA ALA PHE 0.0003358 0.41193 4.34783
22 5KJW 53C 0.008435 0.40691 4.34783
23 1RYD GLC 0.002746 0.43893 4.39277
24 2FQO HYI 0.0144 0.42099 4.4586
25 4OYA 1VE 0.03279 0.43247 4.83092
26 1M15 ARG 0.02028 0.42324 5.31401
27 1M15 ADP 0.02028 0.42324 5.31401
28 3E9I XAH 0.03058 0.40901 5.31401
29 4B0T ADP 0.02519 0.40824 5.31401
30 5TV6 PML 0.0008732 0.44644 5.7971
31 4HWT 1B2 0.007842 0.42628 5.7971
32 5OCA 9QZ 0.01551 0.4003 5.7971
33 1Y7P RIP 0.002482 0.4163 5.8296
34 4NG2 OHN 0.02926 0.40481 6.19469
35 4K55 H6P 0.004436 0.4139 6.45161
36 4KBA 1QM 0.007526 0.4033 6.76329
37 3M3E GAL A2G NPO 0.01064 0.40057 6.8323
38 5DG2 GAL GLC 0.001405 0.43098 8.14815
39 4DXJ IPE 0.02519 0.4159 8.69565
40 4DXJ 0M9 0.02274 0.4159 8.69565
41 4FFG LBS 0.003548 0.42508 10.1449
42 1NCQ W11 0.008528 0.42443 10.2941
43 1SLT NDG GAL 0.004521 0.42676 10.4478
44 3A5Y KAA 0.01348 0.4225 10.628
45 4COQ SAN 0.008138 0.41062 10.628
46 1FM9 9CR 0.02348 0.40366 10.628
47 4TW7 37K 0.01147 0.42764 10.9375
48 4Q3F TLA 0.009163 0.40091 11.1111
49 1REQ DCA 0.03085 0.42189 11.5942
50 4P6X HCY 0.02564 0.40169 11.5942
51 3TTZ 07N 0.004514 0.42979 11.6162
52 4MOB ADP 0.001894 0.4433 12.0773
53 4P8O 883 0.005699 0.40814 12.2995
54 5FPE 3TR 0.003455 0.4232 12.5604
55 1KGI T4A 0.005758 0.44019 12.5984
56 5LRT ADP 0.01314 0.42308 13.0435
57 3GDN FAD 0.04543 0.41249 13.0435
58 1RP0 AHZ 0.03145 0.41182 13.5266
59 1A78 TDG 0.01182 0.40156 16.4179
60 4CS4 AXZ 0.03815 0.41757 16.9082
61 4CS4 ANP 0.03738 0.4128 16.9082
62 1JXM 5GP 0.0000007337 0.63964 23.1884
63 2RCU BUJ 0.01613 0.44475 23.6715
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