Receptor
PDB id Resolution Class Description Source Keywords
2DVO 2.21 Å EC: 3.6.1.19 STRUCTURE OF PH1917 PROTEIN WITH THE COMPLEX OF ITP FROM PYROCOCCUS HORIKOSHII PYROCOCCUS HORIKOSHII NTPASE STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI HYDROLASE
Ref.: STRUCTURES OF DIMERIC NONSTANDARD NUCLEOTIDE TRIPHOSPHATE PYROPHOSPHATASE FROM PYROCOCCUS HORIKOSHII OT3: FUNCTIONAL SIGNIFICANCE OF INTERPROTOMER CONFORMATIONAL CHANGES J.MOL.BIOL. V. 375 1013 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ITT A:201;
 Valid;
 none;
 submit data
508.166 C10 H15 N4 O14 P3 c1nc2...
NA A:301;
 Part of Protein;
 none;
 submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1V7R 1.4 Å EC: 3.6.1.19 STRUCTURE OF NUCLEOTIDE TRIPHOSPHATE PYROPHOSPHATASE FROM PY HORIKOSHII OT3 PYROCOCCUS HORIKOSHII NTPASE STRUCTURAL GENOMICS RIKEN STRUCTURAL GENOMICS/PROTEINITIATIVE RSGI HYDROLASE
Ref.: STRUCTURES OF DIMERIC NONSTANDARD NUCLEOTIDE TRIPHO PYROPHOSPHATASE FROM PYROCOCCUS HORIKOSHII OT3: FUN SIGNIFICANCE OF INTERPROTOMER CONFORMATIONAL CHANGE J.MOL.BIOL. V. 375 1013 2008
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2DVO - ITT C10 H15 N4 O14 P3 c1nc2c(c(n....
2 2DVN - IMP C10 H13 N4 O8 P c1nc2c(n1[....
3 1V7R - CIT C6 H8 O7 C(C(=O)O)C....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2DVO - ITT C10 H15 N4 O14 P3 c1nc2c(c(n....
2 2DVN - IMP C10 H13 N4 O8 P c1nc2c(n1[....
3 1V7R - CIT C6 H8 O7 C(C(=O)O)C....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2DVO - ITT C10 H15 N4 O14 P3 c1nc2c(c(n....
2 2DVN - IMP C10 H13 N4 O8 P c1nc2c(n1[....
3 1V7R - CIT C6 H8 O7 C(C(=O)O)C....
4 2MJP - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ITT; Similar ligands found: 223
No: Ligand ECFP6 Tc MDL keys Tc
1 ITT 1 1
2 ATP 0.730769 0.943662
3 HEJ 0.730769 0.943662
4 5FA 0.721519 0.943662
5 AQP 0.721519 0.943662
6 B4P 0.670886 0.916667
7 AP5 0.670886 0.916667
8 BA3 0.658228 0.916667
9 ADP 0.65 0.943662
10 A2D 0.632911 0.916667
11 AGS 0.630952 0.893333
12 25L 0.623656 0.930556
13 6YZ 0.613636 0.917808
14 HFD 0.604651 0.893333
15 JSQ 0.604651 0.893333
16 AN2 0.583333 0.930556
17 AT4 0.583333 0.905405
18 APR 0.581395 0.916667
19 AR6 0.581395 0.916667
20 TAT 0.579545 0.905405
21 T99 0.579545 0.905405
22 ACQ 0.579545 0.917808
23 ANP 0.579545 0.917808
24 M33 0.576471 0.90411
25 AD9 0.574713 0.917808
26 NO7 0.571429 0.905405
27 HQG 0.571429 0.930556
28 ACP 0.569767 0.917808
29 A22 0.565217 0.930556
30 A 0.555556 0.915493
31 AMP 0.555556 0.915493
32 IMO 0.554217 0.985294
33 ADQ 0.553191 0.891892
34 A3R 0.553191 0.857143
35 ADX 0.54023 0.825
36 CA0 0.54023 0.891892
37 NHD 0.536364 0.90411
38 50T 0.534091 0.90411
39 KG4 0.534091 0.891892
40 ATF 0.532609 0.905405
41 RGT 0.53 0.931507
42 6MZ 0.529412 0.902778
43 7DT 0.52809 0.929577
44 APC 0.52809 0.905405
45 PRX 0.52809 0.842105
46 7D4 0.522727 0.853333
47 A1R 0.520833 0.857143
48 ABM 0.517647 0.864865
49 45A 0.517647 0.864865
50 JNT 0.515464 0.891892
51 AMP MG 0.511905 0.875
52 SRA 0.511905 0.866667
53 CZF 0.51087 0.90411
54 GTP 0.510638 0.868421
55 25A 0.510417 0.916667
56 OAD 0.510204 0.891892
57 9X8 0.510204 0.868421
58 AFH 0.509615 0.835443
59 G5P 0.509615 0.87013
60 AP2 0.505747 0.905405
61 A12 0.505747 0.905405
62 AU1 0.505618 0.917808
63 APC MG 0.505495 0.864865
64 8LE 0.505376 0.844156
65 5AL 0.505376 0.878378
66 6AD 0.505376 0.858974
67 ARU 0.5 0.858974
68 3OD 0.5 0.891892
69 G3A 0.5 0.87013
70 N6P 0.5 0.942029
71 6C6 0.5 0.855263
72 KMQ 0.5 0.88
73 OZV 0.494845 0.916667
74 8LH 0.494737 0.855263
75 SRP 0.494737 0.855263
76 ADP BEF 0.494382 0.888889
77 ADP MG 0.494382 0.888889
78 UP5 0.490741 0.868421
79 GTA 0.490566 0.8375
80 4AD 0.489796 0.868421
81 QBQ 0.489362 0.855263
82 BIS 0.485149 0.881579
83 00A 0.484848 0.833333
84 DLL 0.484848 0.878378
85 QA7 0.484536 0.844156
86 MAP 0.484536 0.893333
87 8LQ 0.484536 0.855263
88 2SA 0.484211 0.905405
89 OOB 0.479592 0.878378
90 8QN 0.479592 0.878378
91 5SV 0.479592 0.8
92 6IA 0.478723 0.8125
93 A4P 0.477477 0.797619
94 B5V 0.475248 0.88
95 WAQ 0.475248 0.833333
96 PAJ 0.474747 0.835443
97 AMO 0.474747 0.88
98 PAP 0.473118 0.929577
99 ADV 0.473118 0.88
100 ATR 0.473118 0.915493
101 ATP MG 0.473118 0.888889
102 RBY 0.473118 0.88
103 ADP PO3 0.473118 0.888889
104 PGS 0.472527 0.881579
105 B5Y 0.471154 0.868421
106 1ZZ 0.470588 0.792683
107 PTJ 0.470588 0.846154
108 AHX 0.47 0.846154
109 T5A 0.469027 0.795181
110 MGP 0.46875 0.835443
111 VO4 ADP 0.46875 0.891892
112 BEF ADP 0.468085 0.864865
113 3UK 0.465347 0.866667
114 6K6 0.464646 0.902778
115 6G0 0.463918 0.835443
116 NAX 0.463636 0.825
117 TXD 0.463636 0.857143
118 DTP 0.463158 0.853333
119 3AT 0.463158 0.916667
120 DQV 0.462963 0.90411
121 2A5 0.462366 0.866667
122 4UV 0.462264 0.844156
123 9SN 0.461538 0.822785
124 7DD 0.461538 0.929577
125 PR8 0.460784 0.802469
126 LAD 0.460784 0.8125
127 OMR 0.459459 0.804878
128 V2G 0.458333 0.846154
129 IDP 0.457447 0.891892
130 B5M 0.457143 0.868421
131 PRT 0.457143 0.90411
132 TXA 0.456311 0.88
133 FYA 0.456311 0.853333
134 K2R 0.456311 0.90411
135 ME8 0.456311 0.792683
136 NB8 0.456311 0.846154
137 139 0.45614 0.825
138 71V 0.455556 0.857143
139 AP0 0.455357 0.846154
140 48N 0.454545 0.846154
141 4UU 0.453704 0.844156
142 HDV 0.453608 0.842105
143 ALF ADP 0.453608 0.820513
144 ANP MG 0.453608 0.878378
145 GP3 0.452632 0.87013
146 ADP BMA 0.45098 0.866667
147 6V0 0.45045 0.846154
148 NAI 0.45045 0.857143
149 DND 0.45045 0.88
150 AVV 0.45 0.846154
151 MGO 0.44898 0.835443
152 GDP 0.447917 0.868421
153 GAP 0.447917 0.842105
154 TXE 0.446429 0.857143
155 SON 0.445652 0.88
156 7D3 0.444444 0.853333
157 A2R 0.444444 0.930556
158 FA5 0.443396 0.855263
159 L3W 0.442478 0.88
160 GA7 0.440367 0.855263
161 DAL AMP 0.44 0.853333
162 GSP 0.44 0.825
163 CNA 0.439655 0.88
164 XAH 0.439252 0.792683
165 7RP 0.438202 0.955882
166 9ZD 0.435644 0.857143
167 9ZA 0.435644 0.857143
168 DDS 0.43299 0.826667
169 LAQ 0.432432 0.792683
170 1RB 0.431818 0.911765
171 LMS 0.431818 0.780488
172 ADJ 0.431034 0.804878
173 NDO 0.430894 0.917808
174 4TC 0.429825 0.846154
175 UPA 0.429825 0.857143
176 80F 0.425 0.795181
177 4UW 0.424779 0.8125
178 F2R 0.423729 0.817073
179 AIR 0.421687 0.847222
180 COD 0.420168 0.767442
181 RMB 0.417582 0.898551
182 AAM 0.417582 0.915493
183 P2P 0.417582 0.956522
184 YLC 0.417391 0.792683
185 ATP A A A 0.416667 0.876712
186 ATP A 0.416667 0.876712
187 YLP 0.415929 0.77381
188 AMZ 0.413793 0.863014
189 C2R 0.413793 0.851351
190 GDC 0.412844 0.835443
191 GDD 0.412844 0.835443
192 GKE 0.412844 0.835443
193 9GM 0.411765 0.846154
194 GNP 0.411765 0.846154
195 D4F 0.41129 0.814815
196 MYR AMP 0.411215 0.771084
197 RBZ 0.411111 0.873239
198 R5I 0.41 0.866667
199 R7I 0.41 0.866667
200 NA7 0.409524 0.905405
201 EAD 0.409449 0.825
202 TYM 0.408696 0.855263
203 A3P 0.408602 0.915493
204 NAD 0.408333 0.878378
205 O02 0.408163 0.87013
206 RAB 0.407407 0.791667
207 ADN 0.407407 0.791667
208 XYA 0.407407 0.791667
209 AOC 0.406593 0.77027
210 YLB 0.405172 0.77381
211 26A 0.404762 0.76
212 NIA 0.404494 0.775
213 5AS 0.404255 0.735632
214 GAV 0.403846 0.835443
215 7RA 0.402174 0.902778
216 JLN 0.402174 0.863014
217 FAI 0.402174 0.863014
218 G1R 0.401961 0.857143
219 JB6 0.401869 0.833333
220 A3D 0.401639 0.866667
221 128 0.4 0.732558
222 PPS 0.4 0.825
223 GNH 0.4 0.857143
Similar Ligands (3D)
Ligand no: 1; Ligand: ITT; Similar ligands found: 1
No: Ligand Similarity coefficient
1 ADP ALF 0.8808
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1V7R; Ligand: CIT; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1v7r.bio1) has 5 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1V7R; Ligand: CIT; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1v7r.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
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