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 (21)
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 2WZC - ALF ADP 3PG n/a n/a
4 1HDI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
5 2XE7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
6 3C3B - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
7 4O3F Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
8 3C3A - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
9 1KF0 Kd = 2.8 mM ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
10 2ZGV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 2WZB - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
12 1VJD Kd = 0.286 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
13 3C3C - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
14 1VJC Kd = 0.263 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
15 2WZD - AF3 ADP 3PG n/a n/a
16 3C39 - 3PG C3 H7 O7 P C([C@H](C(....
17 2XE8 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
18 2YBE - LA8 ALF 3PG n/a n/a
19 2XE6 - 3PG C3 H7 O7 P C([C@H](C(....
20 4O33 Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
21 2P9T - 3PG C3 H7 O7 P C([C@H](C(....
50% Homology Family (27)
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 2WZC - ALF ADP 3PG n/a n/a
7 1HDI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
8 2XE7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
9 3C3B - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
10 4O3F Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
11 3C3A - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
12 1KF0 Kd = 2.8 mM ACP C11 H18 N5 O12 P3 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 1VJC Kd = 0.263 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
18 2WZD - AF3 ADP 3PG n/a n/a
19 3C39 - 3PG C3 H7 O7 P C([C@H](C(....
20 2XE8 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
21 2YBE - LA8 ALF 3PG n/a n/a
22 2XE6 - 3PG C3 H7 O7 P C([C@H](C(....
23 4O33 Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
24 2P9T - 3PG C3 H7 O7 P C([C@H](C(....
25 1VPE - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
26 1PHP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
27 3ZLB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3PG; Similar ligands found: 26
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 M2P 0.424242 0.857143
17 G3H 0.411765 0.9375
18 5RP 0.410256 0.837838
19 D5X 0.410256 0.941176
20 5SP 0.410256 0.837838
21 HMS 0.410256 0.837838
22 0V5 0.40625 0.727273
23 PEQ 0.40625 0.727273
24 RES 0.4 0.659574
25 XBP 0.4 0.885714
26 RUB 0.4 0.885714
Ligand no: 2; Ligand: MAP; Similar ligands found: 274
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 B4P 0.670588 0.92
8 AP5 0.670588 0.92
9 ADP 0.670588 0.945946
10 BA3 0.658824 0.92
11 M33 0.655172 0.907895
12 ABM 0.654762 0.87013
13 ATP 0.647727 0.945946
14 AN2 0.643678 0.959459
15 AMP MG 0.642857 0.894737
16 APR 0.640449 0.92
17 AR6 0.640449 0.92
18 AQP 0.640449 0.945946
19 5FA 0.640449 0.945946
20 APC 0.640449 0.909091
21 A12 0.639535 0.909091
22 AP2 0.639535 0.909091
23 ADX 0.636364 0.831325
24 SRA 0.630952 0.871795
25 ACP 0.629214 0.921053
26 TAT 0.619565 0.909091
27 ACQ 0.619565 0.921053
28 ADP MG 0.617977 0.907895
29 CA0 0.617977 0.896104
30 AD9 0.615385 0.946667
31 AGS 0.615385 0.897436
32 ADV 0.615385 0.884615
33 RBY 0.615385 0.884615
34 SAP 0.615385 0.897436
35 50T 0.611111 0.933333
36 ADP BEF 0.611111 0.884615
37 BEF ADP 0.611111 0.884615
38 ATF 0.606383 0.909091
39 PRX 0.604396 0.848101
40 ANP MG 0.6 0.947368
41 ADP PO3 0.597826 0.893333
42 ATP MG 0.591398 0.907895
43 SRP 0.583333 0.860759
44 5AL 0.578947 0.883117
45 A1R 0.575758 0.8625
46 ALF ADP 0.572917 0.85
47 ADP ALF 0.572917 0.85
48 SON 0.571429 0.884615
49 A22 0.571429 0.933333
50 3OD 0.568627 0.896104
51 GAP 0.568421 0.848101
52 VO4 ADP 0.56701 0.907895
53 ADP VO4 0.56701 0.907895
54 5SV 0.565657 0.807229
55 OAD 0.564356 0.896104
56 AMO 0.56 0.884615
57 ADQ 0.56 0.896104
58 DLL 0.554455 0.883117
59 AHX 0.554455 0.875
60 NB8 0.553398 0.875
61 BIS 0.553398 0.886076
62 25A 0.55 0.92
63 8QN 0.55 0.883117
64 OOB 0.55 0.883117
65 5CD 0.548781 0.763158
66 25L 0.548077 0.933333
67 G5P 0.546296 0.875
68 4AD 0.544554 0.873418
69 PAJ 0.544554 0.841463
70 LAD 0.543689 0.819277
71 5AS 0.543478 0.764045
72 GTA 0.541284 0.843373
73 DAL AMP 0.54 0.858974
74 00A 0.539216 0.839506
75 ME8 0.538462 0.8
76 TXA 0.538462 0.884615
77 1ZZ 0.538462 0.8
78 YAP 0.537736 0.85
79 G3A 0.537037 0.875
80 3UK 0.533981 0.871795
81 ADP BMA 0.533981 0.871795
82 AOC 0.533333 0.779221
83 4UU 0.53211 0.85
84 RAB 0.530864 0.8
85 ADN 0.530864 0.8
86 XYA 0.530864 0.8
87 PR8 0.528846 0.809524
88 WAQ 0.528846 0.839506
89 4UV 0.527778 0.85
90 FYA 0.52381 0.858974
91 PTJ 0.52381 0.851852
92 FA5 0.523364 0.860759
93 MYR AMP 0.518868 0.77907
94 XAH 0.518519 0.821429
95 5N5 0.518072 0.776316
96 PAP 0.515464 0.932432
97 A A 0.514286 0.894737
98 9SN 0.514019 0.829268
99 AMP DBH 0.513761 0.848101
100 UP5 0.513274 0.873418
101 A4D 0.511905 0.776316
102 G5A 0.510204 0.764045
103 A5A 0.51 0.790698
104 JB6 0.509434 0.839506
105 ATP A A A 0.509259 0.881579
106 3DH 0.505618 0.734177
107 TYR AMP 0.504587 0.8375
108 AFH 0.504505 0.841463
109 7MD 0.504505 0.843373
110 YLP 0.504425 0.781609
111 AP0 0.504348 0.851852
112 A3P 0.5 0.918919
113 4UW 0.5 0.819277
114 TAD 0.5 0.841463
115 MTA 0.5 0.734177
116 3AM 0.5 0.88
117 A4P 0.5 0.804598
118 OMR 0.495652 0.811765
119 AHZ 0.495575 0.77907
120 TSB 0.495146 0.802326
121 J7C 0.494624 0.731707
122 7D5 0.494382 0.833333
123 EP4 0.494253 0.716049
124 T5A 0.491525 0.802326
125 4TC 0.491379 0.851852
126 YLB 0.491379 0.781609
127 YLC 0.491379 0.8
128 7MC 0.491379 0.823529
129 48N 0.491228 0.851852
130 AR6 AR6 0.491071 0.87013
131 SSA 0.490196 0.784091
132 2A5 0.489796 0.871795
133 7D3 0.489362 0.858974
134 6RE 0.48913 0.722892
135 M2T 0.488636 0.698795
136 DTA 0.488636 0.746835
137 NAI 0.486957 0.8625
138 TXD 0.486957 0.8625
139 6V0 0.486957 0.851852
140 DND 0.486957 0.884615
141 NAX 0.486957 0.831325
142 NXX 0.486957 0.884615
143 52H 0.485437 0.764045
144 VMS 0.485437 0.772727
145 54H 0.485437 0.772727
146 PPS 0.485149 0.831325
147 ATR 0.484848 0.918919
148 7D4 0.484536 0.858974
149 ITT 0.484536 0.893333
150 A2P 0.484211 0.905405
151 IOT 0.483051 0.793103
152 TYM 0.482759 0.860759
153 TXE 0.482759 0.8625
154 LAQ 0.482456 0.8
155 ARG AMP 0.482456 0.790698
156 5CA 0.480769 0.784091
157 53H 0.480769 0.764045
158 BTX 0.479339 0.802326
159 ADJ 0.478992 0.811765
160 139 0.478992 0.831325
161 YLA 0.478992 0.781609
162 A3N 0.478723 0.746835
163 UPA 0.478632 0.8625
164 YSA 0.477477 0.764045
165 BT5 0.47541 0.793103
166 AYB 0.475 0.772727
167 P5A 0.472222 0.731183
168 NSS 0.471698 0.784091
169 LSS 0.471698 0.747253
170 DSZ 0.471698 0.784091
171 A2R 0.471154 0.933333
172 AF3 ADP 3PG 0.470085 0.819277
173 LA8 ALF 3PG 0.470085 0.819277
174 ALF ADP 3PG 0.470085 0.819277
175 NVA LMS 0.46729 0.747253
176 COD 0.467213 0.775281
177 LPA AMP 0.465517 0.77907
178 IMO 0.463158 0.88
179 LEU LMS 0.462963 0.747253
180 CNA 0.46281 0.884615
181 ZAS 0.462366 0.772152
182 V3L 0.460784 0.92
183 YLY 0.460317 0.772727
184 A3D 0.459677 0.871795
185 KAA 0.458716 0.73913
186 GSU 0.458716 0.764045
187 S4M 0.458333 0.637363
188 GJV 0.458333 0.714286
189 2AM 0.456522 0.893333
190 6AD 0.456311 0.864198
191 NAD 0.455285 0.883117
192 4TA 0.455285 0.770115
193 G A A A 0.455285 0.829268
194 MAO 0.453608 0.744186
195 DSH 0.452632 0.690476
196 5AD 0.452381 0.706667
197 5X8 0.45 0.725
198 NAD IBO 0.447154 0.82716
199 NAE 0.445312 0.85
200 7C5 0.443478 0.777778
201 OVE 0.442105 0.858974
202 DZD 0.44 0.841463
203 U A G G 0.44 0.839506
204 MHZ 0.44 0.685393
205 GNP 0.439252 0.898734
206 N0B 0.438462 0.781609
207 AV2 0.438095 0.894737
208 A3G 0.4375 0.759494
209 NEC 0.4375 0.708861
210 SAI 0.436893 0.719512
211 6C6 0.436893 0.8375
212 NA7 0.436364 0.909091
213 SFG 0.435644 0.7125
214 FB0 0.433824 0.769231
215 WSA 0.433333 0.772727
216 NAJ PZO 0.433071 0.829268
217 3AT 0.432692 0.92
218 6IA 0.432692 0.797619
219 EAD 0.431818 0.831325
220 NAJ PYZ 0.430769 0.831325
221 NAQ 0.430769 0.829268
222 7D7 0.430233 0.705128
223 A7D 0.43 0.7375
224 EEM 0.428571 0.678161
225 SFD 0.428571 0.721649
226 FDA 0.427536 0.795455
227 AMP NAD 0.427481 0.8375
228 ZID 0.427481 0.871795
229 ARU 0.427273 0.819277
230 A5D 0.427184 0.746835
231 SA8 0.427184 0.674419
232 M24 0.426357 0.831325
233 2SA 0.424528 0.884615
234 71V 0.424242 0.8625
235 Z5A 0.424242 0.784091
236 4YB 0.423729 0.747253
237 PO4 PO4 A A A A PO4 0.423423 0.855263
238 A A A 0.423423 0.858974
239 SAH 0.423077 0.707317
240 AVV 0.422018 0.851852
241 DAT 0.421569 0.858974
242 649 0.421488 0.731183
243 SMM 0.420561 0.655556
244 S7M 0.420561 0.659091
245 P1H 0.419118 0.811765
246 DTP 0.419048 0.858974
247 SAM 0.419048 0.659091
248 FAS 0.41844 0.811765
249 FAD 0.41844 0.811765
250 A3S 0.415842 0.769231
251 Y3J 0.41573 0.688312
252 6FA 0.414286 0.802326
253 NDC 0.413043 0.829268
254 GGZ 0.412844 0.785714
255 NJP 0.412698 0.897436
256 101 0.412371 0.833333
257 PGS 0.411765 0.839506
258 SLU 0.410853 0.755556
259 6K6 0.409091 0.881579
260 NDE 0.408759 0.884615
261 D5M 0.408163 0.833333
262 DA 0.408163 0.833333
263 A3T 0.407767 0.779221
264 FNK 0.406897 0.769231
265 AIR 0.406593 0.853333
266 NIA 0.40625 0.82716
267 0UM 0.405405 0.666667
268 AAM 0.40404 0.918919
269 A U 0.403226 0.82716
270 AAT 0.401869 0.674419
271 N6P 0.401786 0.866667
272 TM1 0.4 0.77907
273 AMZ 0.4 0.868421
274 C2R 0.4 0.857143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1QPG; Ligand: MAP; Similar sites found: 28
This union binding pocket(no: 1) in the query (biounit: 1qpg.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2IVD ACJ 0.02094 0.40427 1.20482
2 1YY5 FAD 0.00799 0.41313 1.68675
3 1RSG FAD 0.007895 0.41155 1.68675
4 3VOZ 04A 0.04883 0.40355 1.90476
5 5JBE MAL 0.02483 0.4235 2.16867
6 2GMV PEP 0.04057 0.40137 2.16867
7 3LE7 ADE 0.01741 0.42186 2.29885
8 4I9B 1KA 0.009698 0.42588 2.40964
9 4GKY MAN 0.02384 0.40356 2.68199
10 5IDB MAN 0.0041 0.43992 2.8169
11 5IDB BMA 0.0041 0.43992 2.8169
12 1Q9I TEO 0.01313 0.4122 2.89157
13 1QO8 FAD 0.009603 0.40788 4.09639
14 4WCX ALA 0.01944 0.42643 4.33735
15 2X2T GAL NGA 0.0254 0.41113 4.57516
16 5LFV SIA GAL NAG 0.01726 0.41348 4.73186
17 5L9O GOP 0.003705 0.41403 5.22388
18 1H5R G1P 0.01384 0.40929 5.46075
19 1VBO MAN MAN MAN 0.03666 0.4007 6.71141
20 1I1E DM2 0.03587 0.40014 6.74699
21 5KQA GSH 0.007922 0.4341 6.81818
22 4P6G 2FZ 0.01994 0.40533 7.07965
23 4Z24 FAD 0.01036 0.40646 7.46988
24 3CYQ AMU 0.01513 0.41708 7.97101
25 2VVT DGL 0.01705 0.40489 8.27586
26 1JG3 ADN 0.005266 0.41419 9.78723
27 3IWD M2T 0.01938 0.41369 11.2903
28 2UVO NAG 0.008206 0.43887 12.8655
Pocket No.: 2; Query (leader) PDB : 1QPG; Ligand: 3PG; Similar sites found: 3
This union binding pocket(no: 2) in the query (biounit: 1qpg.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4PIV 2W4 0.01201 0.40357 1.68675
2 5JFS 6K0 0.04069 0.41273 2.27273
3 2PYU IMP 0.007033 0.42128 9.13242
Feedback