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Receptor
PDB id Resolution Class Description Source Keywords
1QPG 2.4 Å EC: 2.7.2.3 3-PHOSPHOGLYCERATE KINASE, MUTATION R65Q SACCHAROMYCES CEREVISIAE PHOSPHOTRANSFERASE (CARBOXYL ACCEPTOR) KINASE ACETYLATIONGLYCOLYSIS
Ref.: STRUCTURE OF THE R65Q MUTANT OF YEAST 3-PHOSPHOGLYCERATE KINASE COMPLEXED WITH MG-AMP-PNP AND 3-PHOSPHO-D-GLYCERATE. BIOCHEMISTRY V. 35 4118 1996
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3PG A:451;
Valid;
none;
submit data
186.057 C3 H7 O7 P C([C@...
MAP A:450;
Valid;
none;
submit data
529.493 C10 H16 Mg N6 O12 P3 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1QPG 2.4 Å EC: 2.7.2.3 3-PHOSPHOGLYCERATE KINASE, MUTATION R65Q SACCHAROMYCES CEREVISIAE PHOSPHOTRANSFERASE (CARBOXYL ACCEPTOR) KINASE ACETYLATIONGLYCOLYSIS
Ref.: STRUCTURE OF THE R65Q MUTANT OF YEAST 3-PHOSPHOGLYCERATE KINASE COMPLEXED WITH MG-AMP-PNP AND 3-PHOSPHO-D-GLYCERATE. BIOCHEMISTRY V. 35 4118 1996
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1QPG - MAP C10 H16 Mg N6 O12 P3 c1nc(c2c(n....
2 3PGK - 3PG C3 H7 O7 P C([C@H](C(....
70% Homology Family (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1QPG - MAP C10 H16 Mg N6 O12 P3 c1nc(c2c(n....
2 3PGK - 3PG C3 H7 O7 P C([C@H](C(....
3 5O7D - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
4 2WZC - ALF ADP 3PG n/a n/a
5 5M3U - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
6 1HDI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
7 2XE7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
8 3C3B - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
9 4O3F Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
10 3C3A - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 1KF0 Kd = 2.8 mM ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
12 5M1R - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
13 2ZGV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 2WZB - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
15 1VJD Kd = 0.286 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
16 3C3C - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
17 5MXM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
18 1VJC Kd = 0.263 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
19 2WZD - AF3 ADP 3PG n/a n/a
20 3C39 - 3PG C3 H7 O7 P C([C@H](C(....
21 2XE8 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
22 2YBE - LA8 ALF 3PG n/a n/a
23 2XE6 - 3PG C3 H7 O7 P C([C@H](C(....
24 4O33 Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
25 5M6Z - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
26 2P9T - 3PG C3 H7 O7 P C([C@H](C(....
50% Homology Family (32)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 13PK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
2 16PK - BIS C15 H22 F4 N5 O12 P3 c1nc(c2c(n....
3 1QPG - MAP C10 H16 Mg N6 O12 P3 c1nc(c2c(n....
4 3PGK - 3PG C3 H7 O7 P C([C@H](C(....
5 2CUN - 3PG C3 H7 O7 P C([C@H](C(....
6 5O7D - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
7 2WZC - ALF ADP 3PG n/a n/a
8 5M3U - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
9 1HDI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
10 2XE7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 3C3B - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
12 4O3F Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
13 3C3A - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 1KF0 Kd = 2.8 mM ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
15 5M1R - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
16 2ZGV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
17 2WZB - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
18 1VJD Kd = 0.286 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
19 3C3C - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
20 5MXM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
21 1VJC Kd = 0.263 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
22 2WZD - AF3 ADP 3PG n/a n/a
23 3C39 - 3PG C3 H7 O7 P C([C@H](C(....
24 2XE8 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
25 2YBE - LA8 ALF 3PG n/a n/a
26 2XE6 - 3PG C3 H7 O7 P C([C@H](C(....
27 4O33 Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
28 5M6Z - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
29 2P9T - 3PG C3 H7 O7 P C([C@H](C(....
30 1VPE - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
31 1PHP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
32 3ZLB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3PG; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 3PG 1 1
2 DEZ 0.575758 0.941176
3 DER 0.575758 0.941176
4 SEP 0.515152 0.74359
5 4TP 0.5 0.780488
6 PA5 0.486486 0.941176
7 R10 0.486486 0.941176
8 DG2 0.485714 0.909091
9 LG6 0.461538 0.941176
10 6PG 0.461538 0.941176
11 HG3 0.451613 0.9375
12 1GP 0.4375 0.852941
13 G3P 0.4375 0.852941
14 PGA 0.433333 0.90625
15 DXP 0.432432 0.911765
16 GOS 0.424242 0.857143
17 M2P 0.424242 0.857143
18 G3H 0.411765 0.9375
19 5SP 0.410256 0.837838
20 D5X 0.410256 0.941176
21 HMS 0.410256 0.837838
22 5RP 0.410256 0.837838
23 0V5 0.40625 0.727273
24 PEQ 0.40625 0.727273
25 RUB 0.4 0.885714
26 XBP 0.4 0.885714
27 RES 0.4 0.659574
Ligand no: 2; Ligand: MAP; Similar ligands found: 289
No: Ligand ECFP6 Tc MDL keys Tc
1 MAP 1 1
2 ANP 0.752941 0.972973
3 AU1 0.73494 0.972973
4 AMP 0.679012 0.918919
5 A 0.679012 0.918919
6 A2D 0.674699 0.92
7 AP5 0.670588 0.92
8 ADP 0.670588 0.945946
9 B4P 0.670588 0.92
10 BA3 0.658824 0.92
11 M33 0.655172 0.907895
12 ABM 0.654762 0.87013
13 HEJ 0.647727 0.945946
14 ATP 0.647727 0.945946
15 AN2 0.643678 0.959459
16 AT4 0.643678 0.909091
17 AQP 0.640449 0.945946
18 APR 0.640449 0.92
19 AR6 0.640449 0.92
20 APC 0.640449 0.909091
21 5FA 0.640449 0.945946
22 A12 0.639535 0.909091
23 AP2 0.639535 0.909091
24 ADX 0.636364 0.831325
25 SRA 0.630952 0.871795
26 ACP 0.629214 0.921053
27 TAT 0.619565 0.909091
28 T99 0.619565 0.909091
29 ACQ 0.619565 0.921053
30 CA0 0.617977 0.896104
31 ADV 0.615385 0.884615
32 AD9 0.615385 0.946667
33 SAP 0.615385 0.897436
34 AGS 0.615385 0.897436
35 RBY 0.615385 0.884615
36 50T 0.611111 0.933333
37 ATF 0.606383 0.909091
38 PRX 0.604396 0.848101
39 6YZ 0.6 0.921053
40 ADP PO3 0.597826 0.893333
41 SRP 0.583333 0.860759
42 9ZA 0.581633 0.886076
43 9ZD 0.581633 0.886076
44 9X8 0.58 0.873418
45 5AL 0.578947 0.883117
46 A1R 0.575758 0.8625
47 ALF ADP 0.572917 0.85
48 ADP ALF 0.572917 0.85
49 A22 0.571429 0.933333
50 SON 0.571429 0.884615
51 3OD 0.568627 0.896104
52 GAP 0.568421 0.848101
53 ADP VO4 0.56701 0.907895
54 VO4 ADP 0.56701 0.907895
55 5SV 0.565657 0.807229
56 OAD 0.564356 0.896104
57 LMS 0.563218 0.809524
58 ADQ 0.56 0.896104
59 A3R 0.56 0.8625
60 AMO 0.56 0.884615
61 DLL 0.554455 0.883117
62 AHX 0.554455 0.875
63 BIS 0.553398 0.886076
64 NB8 0.553398 0.875
65 8QN 0.55 0.883117
66 OOB 0.55 0.883117
67 25A 0.55 0.92
68 5CD 0.548781 0.763158
69 25L 0.548077 0.933333
70 G5P 0.546296 0.875
71 PAJ 0.544554 0.841463
72 4AD 0.544554 0.873418
73 LAD 0.543689 0.819277
74 5AS 0.543478 0.764045
75 GTA 0.541284 0.843373
76 DAL AMP 0.54 0.858974
77 00A 0.539216 0.839506
78 1ZZ 0.538462 0.8
79 ME8 0.538462 0.8
80 TXA 0.538462 0.884615
81 YAP 0.537736 0.85
82 G3A 0.537037 0.875
83 ADP BMA 0.533981 0.871795
84 3UK 0.533981 0.871795
85 AOC 0.533333 0.779221
86 4UU 0.53211 0.85
87 ADN 0.530864 0.8
88 RAB 0.530864 0.8
89 XYA 0.530864 0.8
90 B5V 0.528846 0.860759
91 WAQ 0.528846 0.839506
92 PR8 0.528846 0.809524
93 4UV 0.527778 0.85
94 PTJ 0.52381 0.851852
95 FYA 0.52381 0.858974
96 FA5 0.523364 0.860759
97 MYR AMP 0.518868 0.77907
98 XAH 0.518519 0.821429
99 5N5 0.518072 0.776316
100 PAP 0.515464 0.932432
101 A A 0.514286 0.894737
102 9SN 0.514019 0.829268
103 TYR AMP 0.513761 0.82716
104 AMP DBH 0.513761 0.848101
105 UP5 0.513274 0.873418
106 A4D 0.511905 0.776316
107 G5A 0.510204 0.764045
108 A5A 0.51 0.790698
109 JB6 0.509434 0.839506
110 ATP A A A 0.509259 0.881579
111 B5Y 0.509259 0.85
112 B5M 0.509259 0.85
113 3DH 0.505618 0.734177
114 7MD 0.504505 0.843373
115 GA7 0.504505 0.860759
116 AFH 0.504505 0.841463
117 YLP 0.504425 0.781609
118 AP0 0.504348 0.851852
119 MTA 0.5 0.734177
120 4UW 0.5 0.819277
121 A4P 0.5 0.804598
122 3AM 0.5 0.88
123 A3P 0.5 0.918919
124 DQV 0.5 0.907895
125 TAD 0.5 0.841463
126 OMR 0.495652 0.811765
127 AHZ 0.495575 0.77907
128 TSB 0.495146 0.802326
129 J7C 0.494624 0.731707
130 7D5 0.494382 0.833333
131 EP4 0.494253 0.716049
132 T5A 0.491525 0.802326
133 7MC 0.491379 0.823529
134 4TC 0.491379 0.851852
135 YLB 0.491379 0.781609
136 YLC 0.491379 0.8
137 48N 0.491228 0.851852
138 AR6 AR6 0.491071 0.87013
139 ARG AMP 0.491071 0.790698
140 SSA 0.490196 0.784091
141 2A5 0.489796 0.871795
142 7D3 0.489362 0.858974
143 6RE 0.48913 0.722892
144 M2T 0.488636 0.698795
145 DTA 0.488636 0.746835
146 NAI 0.486957 0.8625
147 6V0 0.486957 0.851852
148 NAX 0.486957 0.831325
149 TXD 0.486957 0.8625
150 DND 0.486957 0.884615
151 NXX 0.486957 0.884615
152 52H 0.485437 0.764045
153 VMS 0.485437 0.772727
154 54H 0.485437 0.772727
155 PPS 0.485149 0.831325
156 ATR 0.484848 0.918919
157 ITT 0.484536 0.893333
158 7D4 0.484536 0.858974
159 A2P 0.484211 0.905405
160 IOT 0.483051 0.793103
161 TXE 0.482759 0.8625
162 TYM 0.482759 0.860759
163 LAQ 0.482456 0.8
164 5CA 0.480769 0.784091
165 8X1 0.480769 0.73913
166 53H 0.480769 0.764045
167 BTX 0.479339 0.802326
168 139 0.478992 0.831325
169 ADJ 0.478992 0.811765
170 YLA 0.478992 0.781609
171 A3N 0.478723 0.746835
172 UPA 0.478632 0.8625
173 YSA 0.477477 0.764045
174 BT5 0.47541 0.793103
175 AYB 0.475 0.772727
176 P5A 0.472222 0.731183
177 DSZ 0.471698 0.784091
178 LSS 0.471698 0.747253
179 NSS 0.471698 0.784091
180 A2R 0.471154 0.933333
181 F2R 0.471074 0.823529
182 AF3 ADP 3PG 0.470085 0.819277
183 NVA LMS 0.46729 0.73913
184 COD 0.467213 0.775281
185 LPA AMP 0.465517 0.77907
186 IMO 0.463158 0.88
187 LEU LMS 0.462963 0.73913
188 CNA 0.46281 0.884615
189 ZAS 0.462366 0.772152
190 V3L 0.460784 0.92
191 YLY 0.460317 0.772727
192 A3D 0.459677 0.871795
193 KAA 0.458716 0.73913
194 GSU 0.458716 0.764045
195 GJV 0.458333 0.714286
196 S4M 0.458333 0.637363
197 2AM 0.456522 0.893333
198 6AD 0.456311 0.864198
199 NAD 0.455285 0.883117
200 G A A A 0.455285 0.829268
201 4TA 0.455285 0.770115
202 9K8 0.454545 0.684211
203 MAO 0.453608 0.744186
204 DSH 0.452632 0.690476
205 5AD 0.452381 0.706667
206 HFD 0.45098 0.897436
207 5X8 0.45 0.725
208 80F 0.448 0.802326
209 NAE 0.445312 0.85
210 AMP NAD 0.443548 0.858974
211 A G 0.443548 0.839506
212 7C5 0.443478 0.777778
213 8PZ 0.442478 0.784091
214 OVE 0.442105 0.858974
215 MHZ 0.44 0.685393
216 DZD 0.44 0.841463
217 U A G G 0.44 0.839506
218 GNP 0.439252 0.898734
219 9GM 0.439252 0.898734
220 N0B 0.438462 0.781609
221 AV2 0.438095 0.894737
222 A3G 0.4375 0.759494
223 NEC 0.4375 0.708861
224 6C6 0.436893 0.8375
225 SAI 0.436893 0.719512
226 NA7 0.436364 0.909091
227 SFG 0.435644 0.7125
228 FB0 0.433824 0.769231
229 WSA 0.433333 0.772727
230 NAJ PZO 0.433071 0.829268
231 U A 0.433071 0.8625
232 3AT 0.432692 0.92
233 6IA 0.432692 0.797619
234 EAD 0.431818 0.831325
235 NAQ 0.430769 0.829268
236 NAJ PYZ 0.430769 0.790698
237 7D7 0.430233 0.705128
238 A7D 0.43 0.7375
239 EEM 0.428571 0.678161
240 SFD 0.428571 0.721649
241 FDA 0.427536 0.795455
242 ZID 0.427481 0.871795
243 ARU 0.427273 0.819277
244 SA8 0.427184 0.674419
245 A5D 0.427184 0.746835
246 M24 0.426357 0.831325
247 2SA 0.424528 0.884615
248 Z5A 0.424242 0.784091
249 71V 0.424242 0.8625
250 4YB 0.423729 0.747253
251 A A A 0.423423 0.858974
252 PO4 PO4 A A A A PO4 0.423423 0.855263
253 SAH 0.423077 0.707317
254 AVV 0.422018 0.851852
255 DAT 0.421569 0.858974
256 649 0.421488 0.731183
257 S7M 0.420561 0.659091
258 SMM 0.420561 0.655556
259 P1H 0.419118 0.811765
260 DTP 0.419048 0.858974
261 SAM 0.419048 0.659091
262 FAS 0.41844 0.811765
263 FAD 0.41844 0.811765
264 A3S 0.415842 0.769231
265 Y3J 0.41573 0.688312
266 6FA 0.414286 0.802326
267 NDC 0.413043 0.829268
268 GGZ 0.412844 0.785714
269 NJP 0.412698 0.897436
270 101 0.412371 0.833333
271 PGS 0.411765 0.839506
272 SLU 0.410853 0.755556
273 6K6 0.409091 0.881579
274 NDE 0.408759 0.884615
275 D5M 0.408163 0.833333
276 DA 0.408163 0.833333
277 A3T 0.407767 0.779221
278 FNK 0.406897 0.769231
279 AIR 0.406593 0.853333
280 8Q2 0.406504 0.758242
281 NIA 0.40625 0.82716
282 0UM 0.405405 0.666667
283 AAM 0.40404 0.918919
284 A U 0.403226 0.82716
285 AAT 0.401869 0.674419
286 N6P 0.401786 0.866667
287 AMZ 0.4 0.868421
288 C2R 0.4 0.857143
289 TM1 0.4 0.77907
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1QPG; Ligand: MAP; Similar sites found with APoc: 82
This union binding pocket(no: 1) in the query (biounit: 1qpg.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 5IXB LGA None
2 2IVD FAD 1.20482
3 2IVD ACJ 1.20482
4 5GLN XYP XYP XYP 1.45349
5 1YY5 FAD 1.68675
6 1RSG FAD 1.68675
7 2G50 ALA 1.68675
8 3VOZ 04A 1.90476
9 4JNA FAD 2.05882
10 5JBE MAL 2.16867
11 2GMV PEP 2.16867
12 1PFK ADP 2.1875
13 3LE7 ADE 2.29885
14 4BTV RB3 2.32558
15 5D63 FUC GLA GLA 2.38908
16 4I9B 1KA 2.40964
17 4GKY MAN 2.68199
18 5IDB BMA 2.8169
19 5IDB MAN 2.8169
20 4L80 OXL 2.87356
21 5BWD FUM 2.89157
22 1Q9I FAD 2.89157
23 1Q9I TEO 2.89157
24 3AYI FAD 2.89157
25 3AYI HCI 2.89157
26 4TQK NAG 2.95567
27 4A59 AMP 3.13253
28 1NAA ABL 3.13253
29 1NAA 6FA 3.13253
30 3KJS NAP 3.13253
31 1Z4O GL1 3.16742
32 2W5P CL8 3.3557
33 4P4M D3T 3.43915
34 3GD8 GOL 3.58744
35 1V84 UDP 3.95257
36 1QO8 FAD 4.09639
37 3ITJ CIT 4.14201
38 4WCX ALA 4.33735
39 5XFI NAG NAG BMA MAN MAN NAG GAL NAG 4.57516
40 2X2T GAL NGA 4.57516
41 2D3N GLC GLC GLC 4.57831
42 6F7L FAD 4.57831
43 5LFV SIA GAL NAG 4.73186
44 2GJP MAL 4.81928
45 5H4S RAM 4.92958
46 1GSU GTX 5.02283
47 3HQP FDP 5.06024
48 2IID PHE 5.06024
49 2IID FAD 5.06024
50 3IWK NAD 5.06024
51 3KIH GDL 5.15464
52 5L9O GOP 5.22388
53 3GU3 SAH 5.28169
54 2OL1 UMP 5.44218
55 1H5R G1P 5.46075
56 2HYQ MAN MAN 5.7377
57 2NU5 NAG 5.7377
58 1H16 DTL 5.78313
59 3VPD BUA 6.0241
60 5YB7 FAD 6.0241
61 5YB7 ORN 6.0241
62 2YG3 FAD 6.26506
63 1VBO MAN MAN MAN 6.71141
64 1I1E DM2 6.74699
65 5KQA GSH 6.81818
66 4P6G 2FZ 7.07965
67 2ZX2 RAM 7.17949
68 1V59 NAD 7.46988
69 4Z24 FAD 7.46988
70 1VMK GUN 7.58123
71 3CYQ AMU 7.97101
72 5LQ8 GB 8.15603
73 2VVT DGL 8.27586
74 3KIF GDL 8.49057
75 3R7F CP 8.88158
76 2PYU IMP 9.13242
77 1JG3 ADN 9.78723
78 5YRJ BGC GLC 9.85915
79 3IWD M2T 11.2903
80 3W6X HZP 11.7904
81 2UVO NAG 12.8655
82 1M26 GAL A2G 13.5338
Pocket No.: 2; Query (leader) PDB : 1QPG; Ligand: 3PG; Similar sites found with APoc: 5
This union binding pocket(no: 2) in the query (biounit: 1qpg.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 4B98 PXG 1.20482
2 4PIV 2W4 1.68675
3 4EN4 GT1 7.37179
4 4EN4 ATP 7.37179
5 2PYU IMP 9.13242
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