Receptor
PDB id Resolution Class Description Source Keywords
4XBA 1.5 Å NON-ENZYME: OTHER HNT3 SCHIZOSACCHAROMYCES POMBE (STRAIN 972 24843) GMP NUCLEOTIDYL TRANSFERASE HYDROLASE
Ref.: DNA3'PP5'G DE-CAPPING ACTIVITY OF APRATAXIN: EFFECT NUCLEOSIDE ANALOGS AND STRUCTURAL BASIS FOR GUANOSI RECOGNITION. NUCLEIC ACIDS RES. V. 43 6075 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GMP A:301;
Valid;
none;
submit data
283.241 C10 H13 N5 O5 c1nc2...
GOL A:303;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
ZN A:302;
B:302;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
5GP B:301;
Valid;
none;
submit data
363.221 C10 H14 N5 O8 P c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4XBA 1.5 Å NON-ENZYME: OTHER HNT3 SCHIZOSACCHAROMYCES POMBE (STRAIN 972 24843) GMP NUCLEOTIDYL TRANSFERASE HYDROLASE
Ref.: DNA3'PP5'G DE-CAPPING ACTIVITY OF APRATAXIN: EFFECT NUCLEOSIDE ANALOGS AND STRUCTURAL BASIS FOR GUANOSI RECOGNITION. NUCLEIC ACIDS RES. V. 43 6075 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 4XBA - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 4XBA - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 4XBA - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GMP; Similar ligands found: 114
No: Ligand ECFP6 Tc MDL keys Tc
1 GMP 1 1
2 5GP 0.732394 0.866667
3 G 0.732394 0.866667
4 3GP 0.704225 0.853333
5 GDP 0.684211 0.88
6 GNH 0.675325 0.868421
7 GP3 0.671053 0.857143
8 GP2 0.662338 0.846154
9 GTP 0.658228 0.88
10 2GP 0.657534 0.866667
11 GDP MG 0.64557 0.833333
12 G2P 0.641975 0.846154
13 GSP 0.641975 0.835443
14 GDP BEF 0.6375 0.8125
15 ALF 5GP 0.6375 0.802469
16 GMV 0.6375 0.857143
17 GPG 0.635294 0.87013
18 GCP 0.62963 0.857143
19 G1R 0.62963 0.868421
20 GAV 0.626506 0.846154
21 GKE 0.625 0.87013
22 GDD 0.625 0.87013
23 GDC 0.625 0.87013
24 GNP 0.621951 0.857143
25 BEF GDP 0.614458 0.802469
26 GTP MG 0.614458 0.833333
27 GCP G 0.607143 0.844156
28 GDP ALF 0.593023 0.802469
29 GDP AF3 0.593023 0.802469
30 G G 0.590909 0.844156
31 G4P 0.588235 0.866667
32 G2R 0.586207 0.846154
33 G3D 0.583333 0.866667
34 P2G 0.576923 0.815789
35 SGP 0.576923 0.78481
36 GFB 0.565217 0.846154
37 GDR 0.565217 0.846154
38 GKD 0.56383 0.87013
39 P1G 0.5625 0.805195
40 0O2 0.561798 0.866667
41 YGP 0.56044 0.792683
42 6CK 0.55914 0.825
43 G3A 0.55914 0.857143
44 Y9Z 0.554348 0.817073
45 G5P 0.553191 0.857143
46 NOS 0.549296 0.940298
47 GTG 0.548387 0.825
48 JB2 0.547368 0.846154
49 GPD 0.541667 0.814815
50 GDX 0.541667 0.857143
51 U2G 0.54 0.848101
52 GDP 7MG 0.536842 0.822785
53 C2E 0.53012 0.828947
54 PCG 0.53012 0.84
55 35G 0.53012 0.84
56 CG2 0.529412 0.848101
57 5GP 5GP 0.52381 0.815789
58 MG7 0.520548 0.957143
59 JB3 0.514852 0.835443
60 G A A A 0.504762 0.857143
61 U A G G 0.5 0.844156
62 FEG 0.495146 0.77381
63 NGD 0.495146 0.846154
64 G U34 0.490385 0.825
65 ZGP 0.490385 0.764706
66 GH3 0.488889 0.855263
67 DGP 0.487805 0.797468
68 DG 0.487805 0.797468
69 G G U 0.484848 0.820513
70 2MD 0.481132 0.785714
71 G C 0.481132 0.835443
72 BGO 0.480769 0.8125
73 GPX 0.478261 0.828947
74 XTS 0.472973 0.913043
75 DGI 0.471264 0.810127
76 CAG 0.46789 0.776471
77 MGD 0.46789 0.785714
78 I2C FE2 CMO CMO 0.463636 0.730337
79 TPG 0.45614 0.741573
80 FE9 0.455357 0.684211
81 4BW 0.454545 0.828947
82 1YD 0.454545 0.828947
83 GGM 0.453704 0.792683
84 G G G RPC 0.453704 0.7875
85 SNI 0.453333 0.898551
86 PGD 0.451327 0.814815
87 MD1 0.451327 0.785714
88 DGT 0.450549 0.810127
89 APC G U 0.45045 0.797468
90 DBG 0.443478 0.835443
91 G1R G1R 0.443478 0.835443
92 13A 0.441558 0.768293
93 GPC 0.441441 0.795181
94 PGD O 0.439655 0.75
95 DG DG 0.43299 0.802469
96 G4M 0.430894 0.797619
97 G G G C 0.429825 0.802469
98 A G C C 0.426087 0.822785
99 U G A 0.424 0.825
100 1YC 0.421569 0.802632
101 AD3 0.421053 0.882353
102 4UR 0.416667 0.828947
103 G C C C 0.411765 0.8125
104 ADN 0.410959 0.882353
105 RAB 0.410959 0.882353
106 XYA 0.410959 0.882353
107 G1G 0.408696 0.814815
108 1DA 0.407895 0.882353
109 AC2 0.407895 0.797297
110 IMP 0.406977 0.84
111 A G U 0.404762 0.825
112 3ZE 0.404494 0.772152
113 MZR 0.402778 0.838235
114 CFE 0.4 0.857143
Ligand no: 2; 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 : 4XBA; Ligand: 5GP; Similar sites found: 55
This union binding pocket(no: 1) in the query (biounit: 4xba.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1NBU PH2 0.002773 0.41771 None
2 5N53 8NB 0.01116 0.41449 1.02564
3 1SQL GUN 0.002759 0.44768 1.36986
4 4Q0L V14 0.01692 0.40144 2
5 3ZW2 GLA NAG GAL FUC 0.009071 0.40393 2.29885
6 3ZW2 NAG GAL FUC 0.00408 0.40271 2.29885
7 3X01 AMP 0.001187 0.46638 2.5
8 5COU ATP 0.00534 0.41237 2.5
9 5BO9 CSF 0.01105 0.4087 2.5
10 5BO9 SIA GAL NGS 0.02292 0.40287 2.5
11 5X1M DHB 0.01821 0.40655 3
12 5UAV TFB 0.02993 0.40149 3
13 5UAV NDP 0.02853 0.40149 3
14 4ITU NAI 0.02776 0.40102 3
15 4ITU 1HS 0.04096 0.40102 3
16 2VHW NAI 0.03328 0.40019 3
17 5MUA GAL 0.0002686 0.48654 3.5
18 4LH7 1X8 0.00265 0.45141 3.5
19 1W2D ADP 0.007422 0.41198 3.5
20 1O44 852 0.02742 0.40536 3.7037
21 2NYR SVR 0.01328 0.44823 4
22 1UNQ 4IP 0.0165 0.40681 4
23 4P5Z Q7M 0.0258 0.4057 4
24 1YQC GLV 0.00115 0.47956 4.11765
25 4JOB TLA 0.001842 0.4179 4.5
26 4JGP PYR 0.0003896 0.42047 5
27 1DMY AZM 0.001764 0.41235 5
28 2ZV2 609 0.00913 0.40771 5
29 4QJP V1F 0.009482 0.41337 6.5
30 4ASE AV9 0.01212 0.41118 7
31 2GQR ADP 0.008778 0.40256 7
32 1UPR 4IP 0.02594 0.40441 7.31707
33 3FW3 ETS 0.009949 0.40593 7.5
34 1X7D ORN 0.03204 0.40198 7.5
35 3VSV XYS 0.004865 0.43836 8
36 1S7G APR 0.01785 0.41046 8
37 2RKV ZBA 0.03221 0.40089 8
38 1Q8A HCS 0.02027 0.40055 8
39 2TPS TPS 0.001639 0.45103 8.5
40 5TO8 7FM 0.01784 0.41467 8.5
41 1F8I GLV 0.01595 0.40952 9
42 2ZQO NGA 0.0005797 0.41285 9.23077
43 1ST0 GTG 0.000005611 0.42393 11.5
44 4QWT ACD 0.0181 0.40148 12
45 3BL7 DD1 0.00153 0.43464 14
46 4INI AMP 0.00000002774 0.64806 15.3846
47 5ETR APC 0.02319 0.40487 15.528
48 5ETR 5RW 0.02319 0.40487 15.528
49 5BV3 M7G 0.00000331 0.56373 16
50 5LNQ CAA 0.01515 0.40789 17.5
51 2Q4H AMP 0.0000002849 0.63142 19
52 4AGQ P96 0.0002626 0.483 19
53 5AVF TAU 0.002922 0.4362 24.5
54 5I2E 67D 0.0000002835 0.66254 34.1085
55 1AV5 AP2 0.0000001495 0.62434 34.9206
Pocket No.: 2; Query (leader) PDB : 4XBA; Ligand: GMP; Similar sites found: 68
This union binding pocket(no: 2) in the query (biounit: 4xba.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1NBU PH2 0.001813 0.43352 None
2 3BJK CIT 0.02675 0.40411 None
3 1YKD CMP 0.01231 0.40162 1
4 1SQL GUN 0.001245 0.46486 1.36986
5 4Q0L V14 0.008737 0.41898 2
6 3X01 AMP 0.001847 0.45431 2.5
7 5COU ATP 0.005191 0.41711 2.5
8 4EN4 GT1 0.02491 0.41087 2.5
9 4EN4 ATP 0.02491 0.41087 2.5
10 4EN4 GT0 0.02491 0.41087 2.5
11 5BO9 SIA GAL NGS 0.02708 0.40271 2.5
12 4AVB CMP 0.007573 0.40504 3
13 5UAV NDP 0.03212 0.40426 3
14 5UAV TFB 0.03212 0.40426 3
15 2VHW NAI 0.03503 0.40233 3
16 5KJZ PCG 0.007907 0.4086 3.33333
17 5MUA GAL 0.0004927 0.47108 3.5
18 4LH7 1X8 0.004637 0.43588 3.5
19 1W2D ADP 0.00602 0.41398 3.5
20 4OTH DRN 0.009203 0.41306 3.5
21 1O44 852 0.02654 0.40946 3.7037
22 2NYR SVR 0.006478 0.46902 4
23 5CDH TLA 0.001064 0.46005 4
24 1UNQ 4IP 0.01545 0.40562 4
25 3AKK ADP 0.01224 0.40362 4
26 1DQS NAD 0.04268 0.40158 4
27 4NJS G08 0.02793 0.40204 4.0404
28 1YQC GLV 0.001381 0.4697 4.11765
29 4JOB TLA 0.001568 0.42159 4.5
30 4GAH 0ET 0.01575 0.40801 4.5
31 4JGP PYR 0.0001973 0.43957 5
32 1DMY AZM 0.002533 0.41434 5
33 4BTV RB3 0.001499 0.40361 5
34 3U2U UDP 0.01812 0.4126 6
35 1NSZ GLC 0.0108 0.40634 6
36 2WHL MAN BMA BMA 0.01547 0.4003 6
37 4QJP V1F 0.004825 0.43146 6.5
38 4P7X AKG 0.008903 0.40823 7
39 4P7X YCP 0.008903 0.40823 7
40 1UPR 4IP 0.01771 0.40908 7.31707
41 3FW3 ETS 0.01187 0.40006 7.5
42 3VSV XYS 0.006353 0.42907 8
43 2TPS TPS 0.005517 0.43018 8.5
44 5TO8 7FM 0.02095 0.4147 8.5
45 2V1O COA 0.01032 0.41696 8.60927
46 3UDZ ADP 0.01093 0.40594 9
47 2ZQO NGA 0.0006386 0.42066 9.23077
48 3P2E SAH 0.014 0.40434 9.33333
49 5BW4 SAM 0.006352 0.4151 10.4869
50 1YC5 NCA 0.01172 0.41703 10.5
51 2CJF RP4 0.01878 0.40137 11.465
52 1ST0 GTG 0.00001574 0.40562 11.5
53 5LRT ADP 0.01466 0.40809 12
54 2GQS ADP 0.009697 0.40447 13.5
55 3BL7 DD1 0.002723 0.42785 14
56 4INI AMP 0.00000001029 0.67793 15.3846
57 5ETR 5RW 0.03235 0.40103 15.528
58 5ETR APC 0.03235 0.40103 15.528
59 4MZQ 1VU 0.01356 0.40152 15.9722
60 5BV3 M7G 0.000007542 0.55463 16
61 1IYK MIM 0.01363 0.41381 17
62 5LNQ CAA 0.01349 0.41404 17.5
63 2Q4H AMP 0.000001404 0.60661 19
64 4AGQ P96 0.0004311 0.47833 19
65 5AVF TAU 0.002781 0.43482 24.5
66 5I2E 67D 0.0000006967 0.65138 34.1085
67 1AV5 AP2 0.00000007486 0.63427 34.9206
68 5RHN 8BR 0.01859 0.41734 36.5217
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