Receptor
PDB id Resolution Class Description Source Keywords
2PEZ 1.4 Å EC: 2.7.1.25 CRYSTAL STRUCTRUE OF DELETION MUTANT OF APS-KINASE DOMAIN OF HUMAN PAPS-SYNTHETASE 1 IN COMPLEX WITH CYCLIC PAPS AND D ADP HOMO SAPIENS NMP-KINASE FOLD PROTEIN IN COMPLEX WITH NUCLEIC ACID TRANSFERASE
Ref.: STRUCTURAL MECHANISM FOR SUBSTRATE INHIBITION OF THE ADENOSINE 5'-PHOSPHOSULFATE KINASE DOMAIN OF HUMAN 3'-PHOSPHOADENOSINE 5'-PHOSPHOSULFATE SYNTHETASE 1 AND ITS RAMIFICATIONS FOR ENZYME REGULATION. J.BIOL.CHEM. V. 282 22112 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DAT A:500;
B:600;
Valid;
Valid;
none;
none;
submit data
411.202 C10 H15 N5 O9 P2 c1nc(...
GGZ A:401;
Valid;
none;
submit data
489.249 C10 H13 N5 O12 P2 S c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2PEZ 1.4 Å EC: 2.7.1.25 CRYSTAL STRUCTRUE OF DELETION MUTANT OF APS-KINASE DOMAIN OF HUMAN PAPS-SYNTHETASE 1 IN COMPLEX WITH CYCLIC PAPS AND D ADP HOMO SAPIENS NMP-KINASE FOLD PROTEIN IN COMPLEX WITH NUCLEIC ACID TRANSFERASE
Ref.: STRUCTURAL MECHANISM FOR SUBSTRATE INHIBITION OF THE ADENOSINE 5'-PHOSPHOSULFATE KINASE DOMAIN OF HUMAN 3'-PHOSPHOADENOSINE 5'-PHOSPHOSULFATE SYNTHETASE 1 AND ITS RAMIFICATIONS FOR ENZYME REGULATION. J.BIOL.CHEM. V. 282 22112 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2PEZ - GGZ C10 H13 N5 O12 P2 S c1nc(c2c(n....
2 2PEY - DAT C10 H15 N5 O9 P2 c1nc(c2c(n....
70% 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 2PEZ - GGZ C10 H13 N5 O12 P2 S c1nc(c2c(n....
2 2PEY - DAT C10 H15 N5 O9 P2 c1nc(c2c(n....
3 2OFW Ki = 17 uM ADX C10 H14 N5 O10 P S c1nc(c2c(n....
4 2OFX - PPS C10 H15 N5 O13 P2 S c1nc(c2c(n....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2PEZ - GGZ C10 H13 N5 O12 P2 S c1nc(c2c(n....
2 2PEY - DAT C10 H15 N5 O9 P2 c1nc(c2c(n....
3 5CB8 Ki = 18.2 uM ADX C10 H14 N5 O10 P S c1nc(c2c(n....
4 3UIE - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
5 2OFW Ki = 17 uM ADX C10 H14 N5 O10 P S c1nc(c2c(n....
6 2OFX - PPS C10 H15 N5 O13 P2 S c1nc(c2c(n....
7 1M7G - ADX C10 H14 N5 O10 P S c1nc(c2c(n....
8 1M7H - ADX C10 H14 N5 O10 P S c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DAT; Similar ligands found: 182
No: Ligand ECFP6 Tc MDL keys Tc
1 DAT 1 1
2 DTP 0.891892 1
3 DA 0.816901 0.971831
4 D5M 0.816901 0.971831
5 DZ4 0.740741 0.972603
6 AS 0.733333 0.92
7 3L1 0.661972 0.835616
8 3D1 0.661972 0.835616
9 CUU 0.638554 0.931507
10 7D3 0.617284 0.893333
11 DDS 0.609195 0.944444
12 CPA 0.607843 0.8625
13 HF7 0.606742 0.986111
14 ADP 0.60241 0.905405
15 5F1 0.6 0.794521
16 PAP 0.586207 0.917808
17 101 0.580247 0.917808
18 2A5 0.574713 0.932432
19 3AT 0.573034 0.931507
20 ATR 0.568182 0.930556
21 6MA 0.564706 0.931507
22 DOI 0.564706 0.917808
23 7D4 0.551724 0.893333
24 ATP 0.545455 0.905405
25 HEJ 0.545455 0.905405
26 AV2 0.543478 0.88
27 5FA 0.539326 0.905405
28 AQP 0.539326 0.905405
29 DGI 0.538462 0.909091
30 ZDA 0.533333 0.853333
31 103 0.53012 0.826667
32 A2D 0.529412 0.88
33 B4P 0.528736 0.88
34 AP5 0.528736 0.88
35 BA3 0.517241 0.88
36 7D5 0.512195 0.866667
37 AT4 0.505618 0.87013
38 AN2 0.505618 0.893333
39 ACQ 0.505376 0.906667
40 6YZ 0.505263 0.906667
41 6OG 0.5 0.907895
42 M33 0.5 0.868421
43 ACP 0.494505 0.906667
44 AMP 0.494118 0.878378
45 A 0.494118 0.878378
46 T99 0.489362 0.87013
47 ANP 0.489362 0.881579
48 TAT 0.489362 0.87013
49 APR 0.48913 0.88
50 AR6 0.48913 0.88
51 A1R 0.484848 0.921053
52 DGT 0.484536 0.909091
53 PPS 0.484211 0.817073
54 AGS 0.483871 0.858974
55 AD9 0.483871 0.881579
56 ADX 0.483516 0.795181
57 CA0 0.483516 0.857143
58 A3P 0.483146 0.90411
59 KG4 0.478261 0.857143
60 ABM 0.477273 0.831169
61 45A 0.477273 0.831169
62 NA7 0.475248 0.945946
63 PRX 0.473118 0.833333
64 APC 0.473118 0.92
65 AMP MG 0.471264 0.84
66 A3R 0.47 0.921053
67 HQG 0.469388 0.893333
68 A2R 0.469388 0.893333
69 A2P 0.466667 0.916667
70 A22 0.464646 0.893333
71 ATF 0.463918 0.87013
72 MDR 0.463415 0.783784
73 50T 0.462366 0.868421
74 25L 0.461538 0.893333
75 ADP BEF 0.456522 0.853333
76 ADP MG 0.456522 0.853333
77 ADQ 0.455446 0.857143
78 12D 0.454545 0.755814
79 5AL 0.453608 0.844156
80 8LE 0.453608 0.8125
81 2AM 0.453488 0.90411
82 T5A 0.452174 0.853659
83 A12 0.450549 0.92
84 AP2 0.450549 0.92
85 QA7 0.45 0.8125
86 3AM 0.448276 0.864865
87 8LH 0.444444 0.822785
88 SRP 0.444444 0.87013
89 4AD 0.441176 0.883117
90 3AD 0.439024 0.77027
91 SRA 0.438202 0.833333
92 OVE 0.438202 0.868421
93 NB8 0.438095 0.860759
94 3OD 0.438095 0.857143
95 KF5 0.4375 0.635135
96 APC MG 0.4375 0.855263
97 ADP PO3 0.4375 0.853333
98 ATP MG 0.4375 0.853333
99 DLL 0.436893 0.844156
100 JNT 0.436893 0.906667
101 00A 0.436893 0.802469
102 AU1 0.43617 0.881579
103 8LQ 0.435644 0.846154
104 GGZ 0.435644 0.792683
105 ANP MG 0.434343 0.844156
106 ALF ADP 0.434343 0.790123
107 128 0.433628 0.747126
108 BEF ADP 0.43299 0.831169
109 9X8 0.432692 0.835443
110 OAD 0.432692 0.857143
111 25A 0.431373 0.88
112 OOB 0.431373 0.844156
113 5SV 0.431373 0.814815
114 OZV 0.431373 0.88
115 8QN 0.431373 0.844156
116 2FD 0.430233 0.805195
117 9SN 0.429907 0.792683
118 PR8 0.428571 0.8625
119 V3L 0.428571 0.88
120 GAP 0.428571 0.810127
121 WAQ 0.428571 0.871795
122 AMO 0.427184 0.894737
123 PAJ 0.427184 0.804878
124 DG 0.425532 0.896104
125 DGP 0.425532 0.896104
126 7D7 0.425 0.733333
127 PTJ 0.424528 0.814815
128 1ZZ 0.424528 0.807229
129 FYA 0.424528 0.893333
130 BIS 0.424528 0.848101
131 RBY 0.42268 0.894737
132 ADV 0.42268 0.894737
133 MAP 0.421569 0.858974
134 NAI 0.421053 0.825
135 6V0 0.421053 0.814815
136 VO4 ADP 0.42 0.857143
137 8DD 0.42 0.921053
138 ADN 0.419753 0.76
139 RAB 0.419753 0.76
140 XYA 0.419753 0.76
141 3UK 0.419048 0.833333
142 CL9 0.418605 0.805195
143 139 0.415254 0.8625
144 NDP 0.415254 0.8375
145 LAD 0.415094 0.85
146 B5V 0.415094 0.822785
147 J4G 0.415094 0.883117
148 ADS THS THS THS 0.414634 0.770115
149 AP0 0.413793 0.814815
150 KMQ 0.412844 0.846154
151 FA5 0.412844 0.87013
152 NZQ 0.411765 0.85
153 ME8 0.411215 0.807229
154 TXA 0.411215 0.846154
155 G5P 0.410714 0.8375
156 SON 0.410526 0.894737
157 7DD 0.410526 0.891892
158 A4P 0.410256 0.790698
159 6AD 0.41 0.82716
160 V2G 0.41 0.860759
161 AHX 0.409524 0.860759
162 J7V 0.409449 0.761364
163 TXD 0.408696 0.848101
164 UP5 0.408696 0.835443
165 YYY 0.408602 0.831169
166 DAL AMP 0.407767 0.820513
167 HDV 0.405941 0.881579
168 ADP BMA 0.40566 0.833333
169 TXE 0.405172 0.848101
170 0WD 0.404959 0.8375
171 HFD 0.40404 0.858974
172 JSQ 0.40404 0.858974
173 N5P 0.403846 0.797468
174 LAQ 0.403509 0.807229
175 G3A 0.401786 0.8375
176 48N 0.4 0.8375
177 TXP 0.4 0.860759
178 ARJ 0.4 0.693333
179 ZZB 0.4 0.744186
180 B5M 0.4 0.8125
181 B5Y 0.4 0.8125
182 PUA 0.4 0.897436
Ligand no: 2; Ligand: GGZ; Similar ligands found: 140
No: Ligand ECFP6 Tc MDL keys Tc
1 GGZ 1 1
2 LQJ 0.708333 0.825
3 ACK 0.658537 0.818182
4 ADX 0.617977 0.949367
5 PPS 0.578947 0.949367
6 AV2 0.525253 0.848101
7 QQY 0.511111 0.822785
8 QQX 0.5 0.835443
9 A2D 0.494624 0.825
10 7D5 0.494382 0.746988
11 OZV 0.490385 0.848101
12 7D3 0.489362 0.771084
13 BA3 0.484211 0.825
14 50T 0.479592 0.792683
15 B4P 0.479167 0.825
16 ADP 0.479167 0.825
17 AP5 0.479167 0.825
18 AMP 0.478261 0.8
19 A 0.478261 0.8
20 AT4 0.474227 0.839506
21 AN2 0.474227 0.814815
22 AD9 0.47 0.804878
23 12D 0.469565 0.733333
24 CA0 0.469388 0.804878
25 7D4 0.469388 0.771084
26 M33 0.469388 0.814815
27 KG4 0.464646 0.804878
28 ACP 0.464646 0.804878
29 ATP 0.464646 0.825
30 HEJ 0.464646 0.825
31 45A 0.463158 0.780488
32 ABM 0.463158 0.780488
33 128 0.461538 0.725275
34 PRX 0.46 0.761905
35 2A5 0.46 0.783133
36 AR6 0.46 0.825
37 AQP 0.46 0.825
38 APR 0.46 0.825
39 5FA 0.46 0.825
40 AMP MG 0.457447 0.7875
41 PAP 0.455446 0.835443
42 ATR 0.455446 0.846154
43 AGS 0.455446 0.851852
44 GPX 0.453704 0.804878
45 AP2 0.453608 0.795181
46 A2P 0.453608 0.833333
47 A3P 0.453608 0.822785
48 A12 0.453608 0.795181
49 TM1 0.45045 0.722222
50 ACQ 0.446602 0.804878
51 ANP 0.446602 0.804878
52 5AL 0.442308 0.792683
53 8LE 0.442308 0.764706
54 SRA 0.442105 0.82716
55 2AM 0.44086 0.822785
56 AU1 0.44 0.804878
57 8LQ 0.439252 0.77381
58 ATF 0.438095 0.795181
59 3AM 0.43617 0.7875
60 CUU 0.435644 0.825
61 DAT 0.435644 0.792683
62 8LH 0.433962 0.77381
63 6YZ 0.433962 0.804878
64 SRP 0.433962 0.77381
65 TAT 0.432692 0.839506
66 T99 0.432692 0.839506
67 APC 0.431373 0.795181
68 4AD 0.431193 0.785714
69 7D7 0.430233 0.646341
70 ADP BEF 0.43 0.8
71 ADP MG 0.43 0.8
72 HQG 0.429907 0.814815
73 A2R 0.429907 0.814815
74 DLL 0.427273 0.792683
75 APC MG 0.427184 0.780488
76 RBY 0.427184 0.795181
77 ADV 0.427184 0.795181
78 OVE 0.427083 0.8375
79 QA7 0.425926 0.764706
80 A22 0.425926 0.814815
81 NA7 0.423423 0.795181
82 DA 0.42268 0.768293
83 D5M 0.42268 0.768293
84 OOB 0.422018 0.792683
85 8QN 0.422018 0.792683
86 25A 0.422018 0.802469
87 5SV 0.422018 0.727273
88 KL2 0.419355 0.775
89 3AT 0.419048 0.825
90 V3L 0.419048 0.802469
91 DTP 0.419048 0.792683
92 AMO 0.418182 0.795181
93 ADQ 0.418182 0.804878
94 PAJ 0.418182 0.758621
95 A1R 0.418182 0.776471
96 A3R 0.418182 0.776471
97 LMS 0.416667 0.901235
98 ZZB 0.416 0.703297
99 TXA 0.415929 0.795181
100 SON 0.415842 0.77381
101 ANZ 0.415254 0.744186
102 V2G 0.415094 0.747126
103 00A 0.414414 0.755814
104 JNT 0.414414 0.804878
105 AHX 0.414414 0.767442
106 ATP MG 0.413462 0.8
107 ADP PO3 0.413462 0.8
108 MAP 0.412844 0.785714
109 ALF ADP 0.411215 0.744186
110 3UK 0.410714 0.783133
111 OAD 0.410714 0.804878
112 9X8 0.410714 0.829268
113 CMP 0.41 0.78481
114 2BA 0.41 0.797468
115 BEF ADP 0.409524 0.780488
116 XYA 0.409091 0.7125
117 RAB 0.409091 0.7125
118 ADN 0.409091 0.7125
119 B5V 0.40708 0.77381
120 LAD 0.40708 0.738636
121 PR8 0.40708 0.730337
122 WAQ 0.40708 0.755814
123 J4G 0.40708 0.764706
124 DDS 0.40566 0.790123
125 GAP 0.40566 0.761905
126 B5M 0.405172 0.764706
127 J7C 0.40404 0.636364
128 1ZZ 0.403509 0.722222
129 BIS 0.403509 0.776471
130 FYA 0.403509 0.771084
131 3OD 0.403509 0.804878
132 NB8 0.403509 0.767442
133 ME8 0.403509 0.741573
134 PTJ 0.403509 0.747126
135 NAX 0.401639 0.75
136 F2R 0.401575 0.725275
137 5N5 0.4 0.691358
138 DQV 0.4 0.814815
139 25L 0.4 0.814815
140 GTA 0.4 0.741573
Similar Ligands (3D)
Ligand no: 1; Ligand: DAT; Similar ligands found: 39
No: Ligand Similarity coefficient
1 GDP 0.9680
2 GNH 0.9480
3 TYD 0.9300
4 ADP AF3 0.9270
5 M7G 0.9211
6 BEF GDP 0.9208
7 GDP AF3 0.9208
8 DUD 0.9204
9 UDP 0.9189
10 GDP MG 0.9159
11 DUN 0.9041
12 CDP 0.9016
13 NYZ 0.8993
14 GP2 0.8985
15 UC5 0.8976
16 IDP 0.8963
17 GJV 0.8936
18 8GD 0.8912
19 O02 0.8898
20 NWZ 0.8889
21 7DT 0.8871
22 G5A 0.8839
23 NO7 0.8814
24 NX8 0.8812
25 GNP 0.8750
26 GCQ 0.8738
27 SAH 0.8738
28 GSP 0.8737
29 J7C 0.8700
30 G3D 0.8697
31 UDP UDP 0.8691
32 IMP 0.8679
33 5GP 0.8677
34 SAM 0.8676
35 GTP 0.8669
36 6RE 0.8669
37 GCP 0.8646
38 FMP 0.8623
39 G 0.8522
Ligand no: 2; Ligand: GGZ; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2PEZ; Ligand: DAT; Similar sites found with APoc: 12
This union binding pocket(no: 1) in the query (biounit: 2pez.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 2VVG ADP 5.58659
2 2VVG ADP 5.58659
3 1GOJ ADP 6.14525
4 2AWN ADP 6.70391
5 2AWN ADP 6.70391
6 2AWN ADP 6.70391
7 2AWN ADP 6.70391
8 4CVN ADP 8.37989
9 4CVN ADP 8.37989
10 2PZE ATP 8.37989
11 3A4M ADP 39.1061
12 3A4M ADP 39.1061
Pocket No.: 2; Query (leader) PDB : 2PEZ; Ligand: DAT; Similar sites found with APoc: 5
This union binding pocket(no: 2) in the query (biounit: 2pez.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 2VVG ADP 5.58659
2 1GOJ ADP 6.14525
3 1LVG ADP 6.70391
4 4CVN ADP 8.37989
5 4CVN ADP 8.37989
Pocket No.: 3; Query (leader) PDB : 2PEZ; Ligand: GGZ; Similar sites found with APoc: 12
This union binding pocket(no: 3) in the query (biounit: 2pez.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 2VVG ADP 5.58659
2 2VVG ADP 5.58659
3 1GOJ ADP 6.14525
4 2AWN ADP 6.70391
5 2AWN ADP 6.70391
6 2AWN ADP 6.70391
7 2AWN ADP 6.70391
8 4CVN ADP 8.37989
9 4CVN ADP 8.37989
10 2PZE ATP 8.37989
11 3A4M ADP 39.1061
12 3A4M ADP 39.1061
APoc FAQ
Feedback