Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:300;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 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: GDP; Similar ligands found: 153
No: Ligand ECFP6 Tc MDL keys Tc
1 GDP 1 1
2 GTP 0.909091 1
3 GP3 0.881579 0.973684
4 GNH 0.858974 0.986667
5 GNP 0.839506 0.973684
6 G 0.828947 0.986486
7 5GP 0.828947 0.986486
8 G1R 0.82716 0.986667
9 GCP 0.82716 0.973684
10 GSP 0.817073 0.948718
11 GAV 0.797619 0.961039
12 GMV 0.792683 0.973684
13 G2P 0.77381 0.961039
14 G2R 0.770115 0.961039
15 GDP MG 0.759036 0.923077
16 GP2 0.756098 0.961039
17 GDP BEF 0.75 0.9
18 GDD 0.747253 0.961039
19 GKE 0.747253 0.961039
20 GDC 0.747253 0.961039
21 GPG 0.741573 0.961039
22 G3D 0.732558 0.986486
23 ALF 5GP 0.729412 0.888889
24 Y9Z 0.728261 0.902439
25 GTP MG 0.724138 0.923077
26 BEF GDP 0.724138 0.888889
27 G5P 0.723404 0.973684
28 GFB 0.72043 0.961039
29 GTG 0.72043 0.936709
30 GDR 0.72043 0.961039
31 G4P 0.715909 0.986486
32 GCP G 0.715909 0.935065
33 6CK 0.712766 0.936709
34 G3A 0.712766 0.973684
35 GDP ALF 0.7 0.888889
36 GDP AF3 0.7 0.888889
37 YGP 0.698925 0.901235
38 JB2 0.697917 0.961039
39 GKD 0.697917 0.961039
40 GDX 0.690722 0.973684
41 GPD 0.690722 0.925
42 GMP 0.684211 0.88
43 0O2 0.666667 0.986486
44 G G 0.659574 0.935065
45 JB3 0.656863 0.948718
46 NGD 0.650485 0.961039
47 GDP 7MG 0.636364 0.911392
48 DGI 0.636364 0.923077
49 U2G 0.634615 0.936709
50 GPX 0.634409 0.946667
51 IDP 0.632184 0.972973
52 2MD 0.632075 0.891566
53 CAG 0.62963 0.880952
54 CG2 0.622642 0.936709
55 FEG 0.619048 0.879518
56 MGD 0.614679 0.891566
57 ZGP 0.613208 0.869048
58 GH3 0.612903 0.973333
59 3GP 0.611765 0.946667
60 MD1 0.607143 0.891566
61 PGD 0.59292 0.925
62 DGT 0.591398 0.923077
63 BGO 0.588785 0.924051
64 TPG 0.582609 0.840909
65 DBG 0.582609 0.948718
66 2GP 0.574713 0.96
67 FE9 0.570175 0.776596
68 I2C FE2 CMO CMO 0.566372 0.808989
69 G A A A 0.553571 0.923077
70 MGP 0.553191 0.961039
71 U A G G 0.548673 0.935065
72 G4M 0.548387 0.880952
73 6G0 0.547368 0.961039
74 G1R G1R 0.542373 0.924051
75 P2G 0.527473 0.883117
76 PGD O 0.525 0.850575
77 ADP 0.522222 0.92
78 GGM 0.517544 0.901235
79 DG 0.516484 0.910256
80 DGP 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G G U 0.509259 0.935065
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 G C 0.504348 0.9
86 GPC 0.491525 0.879518
87 G7M 0.483871 0.948052
88 6AD 0.479592 0.841463
89 ATP 0.473684 0.92
90 G2Q 0.471154 0.961039
91 U G A 0.469697 0.888889
92 5FA 0.46875 0.92
93 AQP 0.46875 0.92
94 GTA 0.468468 0.936709
95 7DD 0.468085 0.906667
96 G G G RPC 0.466102 0.875
97 SGP 0.463158 0.82716
98 01G 0.462963 0.902439
99 B4P 0.457447 0.894737
100 AP5 0.457447 0.894737
101 A2D 0.456522 0.894737
102 G G G C 0.455285 0.9125
103 ACQ 0.454545 0.896104
104 5GP 5GP 0.454545 0.883117
105 ANP 0.454545 0.896104
106 A G C C 0.451613 0.911392
107 APC G U 0.45082 0.886076
108 G U34 0.449153 0.888889
109 DG DG 0.448598 0.865854
110 ITT 0.447917 0.868421
111 BA3 0.446809 0.894737
112 35G 0.444444 0.933333
113 C2E 0.444444 0.921053
114 PCG 0.444444 0.933333
115 MGO 0.441176 0.864198
116 AN2 0.4375 0.907895
117 G C C C 0.4375 0.924051
118 M33 0.43299 0.883117
119 UCG 0.429688 0.911392
120 A G U 0.42963 0.888889
121 ACP 0.428571 0.896104
122 MGQ 0.424528 0.935897
123 7DT 0.424242 0.906667
124 APR 0.424242 0.894737
125 AR6 0.424242 0.894737
126 93A 0.42268 0.833333
127 A4P 0.420168 0.869048
128 SAP 0.42 0.873418
129 AD9 0.42 0.896104
130 AGS 0.42 0.873418
131 G8D 0.42 0.875
132 CA0 0.418367 0.896104
133 ATF 0.417476 0.884615
134 AGO 0.414634 0.888889
135 NIA 0.413043 0.82716
136 MGV 0.412844 0.890244
137 TAT 0.411765 0.884615
138 A1R 0.411215 0.839506
139 ADQ 0.411215 0.871795
140 RGT 0.410714 0.909091
141 CGP 0.409836 0.86747
142 AMP 0.408602 0.893333
143 A 0.408602 0.893333
144 UP5 0.40678 0.873418
145 C2R 0.406593 0.906667
146 AMZ 0.406593 0.918919
147 JBT 0.405882 0.778947
148 A22 0.40566 0.907895
149 25L 0.405405 0.907895
150 ADX 0.40404 0.809524
151 8OD 0.401961 0.946667
152 4TC 0.4 0.851852
153 50T 0.4 0.883117
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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