Receptor
PDB id Resolution Class Description Source Keywords
2RKD 1.9 Å EC: 4.1.1.32 THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH 3- PHOSPHONOPROPIONATE RATTUS NORVEGICUS KINASE GLUCONEOGENESIS LYASE DECARBOXYLASE GTP-BINDING NUCLEOTIDE-BINDING
Ref.: DIFFERENTIAL INHIBITION OF CYTOSOLIC PEPCK BY SUBST ANALOGUES. KINETIC AND STRUCTURAL CHARACTERIZATION INHIBITOR RECOGNITION. BIOCHEMISTRY V. 47 2099 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3PP A:703;
Valid;
none;
Ki = 1.9 mM
154.058 C3 H7 O5 P C(CP(...
MN A:700;
A:701;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
NA A:702;
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
1NHX 2.1 Å EC: 4.1.1.32 PEPCK COMPLEX WITH A GTP-COMPETITIVE INHIBITOR HOMO SAPIENS GLUCONEOGENESIS XANTHINE INHIBITOR LYASE
Ref.: X-RAY STRUCTURES OF TWO XANTHINE INHIBITORS BOUND TO PEPCK AND N-3 MODIFICATIONS OF SUBSTITUTED 1,8-DIBENZYLXANTHINES BIOORG.MED.CHEM.LETT. V. 13 3871 2003
Members (44)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4GMW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 4GNO - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 5FH1 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
4 4GNL - PEP C3 H5 O6 P C=C(C(=O)O....
5 4GNP - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 3DT2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
7 6P5O ic50 = 97 uM O2Y C8 H7 N O4 S c1cc(c(nc1....
8 5V9H - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 3MOF Ki = 860 uM OXL C2 O4 C(=O)(C(=O....
10 4GNQ - OXL C2 O4 C(=O)(C(=O....
11 2QF2 - OAA C4 H3 O5 C(C(=O)C(=....
12 4GMM - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
13 3DT7 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
14 3DTB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 5FH3 Ki = 970 uM OXL C2 O4 C(=O)(C(=O....
16 4GMU - OXL C2 O4 C(=O)(C(=O....
17 1KHF - PEP C3 H5 O6 P C=C(C(=O)O....
18 4YW8 - 1WD C6 H5 N O2 S c1cc(c(nc1....
19 4YWD - NTM C7 H5 N O4 c1cc(c(nc1....
20 5FH4 Ki = 174 uM SPV C3 H4 O6 S C(C(=O)C(=....
21 2RKD Ki = 1.9 mM 3PP C3 H7 O5 P C(CP(=O)(O....
22 3MOH Ki = 1460 uM PGA C2 H5 O6 P C(C(=O)O)O....
23 2RK8 Ki = 230 uM PPF C H3 O5 P C(=O)(O)P(....
24 5V9G Ki = 441 uM OXL C2 O4 C(=O)(C(=O....
25 5FH5 - PGA C2 H5 O6 P C(C(=O)O)O....
26 5V9F Ki = 37 uM SPV C3 H4 O6 S C(C(=O)C(=....
27 4YW9 Ki = 45 uM 1WD C6 H5 N O2 S c1cc(c(nc1....
28 3MOE Ki = 50 uM SPV C3 H4 O6 S C(C(=O)C(=....
29 2RK7 Ki = 89 uM OXL C2 O4 C(=O)(C(=O....
30 4GNM - OXL C2 O4 C(=O)(C(=O....
31 2QF1 - OAA C4 H3 O5 C(C(=O)C(=....
32 5FH2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
33 2RKA Ki = 1 mM PGA C2 H5 O6 P C(C(=O)O)O....
34 1M51 ic50 = 18.8 uM TSX C21 H25 N5 O3 CCCCN1c2c(....
35 1NHX ic50 = 2.11 uM FTB C25 H26 F N5 O3 CCCCN1c2c(....
36 4GMZ - SPV C3 H4 O6 S C(C(=O)C(=....
37 4OX2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
38 5FH0 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
39 5V97 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
40 1KHB - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
41 3DT4 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
42 2RKE Ki = 82.5 uM SAT C2 H4 O5 S C(C(=O)O)S....
43 2QEY - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
44 4YWB - OXD C2 H2 O4 C(=O)(C(=O....
70% Homology Family (48)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4GMW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 4GNO - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 5FH1 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
4 4GNL - PEP C3 H5 O6 P C=C(C(=O)O....
5 4GNP - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 3DT2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
7 6P5O ic50 = 97 uM O2Y C8 H7 N O4 S c1cc(c(nc1....
8 5V9H - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 3MOF Ki = 860 uM OXL C2 O4 C(=O)(C(=O....
10 4GNQ - OXL C2 O4 C(=O)(C(=O....
11 2QF2 - OAA C4 H3 O5 C(C(=O)C(=....
12 4GMM - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
13 3DT7 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
14 3DTB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 5FH3 Ki = 970 uM OXL C2 O4 C(=O)(C(=O....
16 4GMU - OXL C2 O4 C(=O)(C(=O....
17 1KHF - PEP C3 H5 O6 P C=C(C(=O)O....
18 4YW8 - 1WD C6 H5 N O2 S c1cc(c(nc1....
19 4YWD - NTM C7 H5 N O4 c1cc(c(nc1....
20 5FH4 Ki = 174 uM SPV C3 H4 O6 S C(C(=O)C(=....
21 2RKD Ki = 1.9 mM 3PP C3 H7 O5 P C(CP(=O)(O....
22 3MOH Ki = 1460 uM PGA C2 H5 O6 P C(C(=O)O)O....
23 2RK8 Ki = 230 uM PPF C H3 O5 P C(=O)(O)P(....
24 5V9G Ki = 441 uM OXL C2 O4 C(=O)(C(=O....
25 5FH5 - PGA C2 H5 O6 P C(C(=O)O)O....
26 5V9F Ki = 37 uM SPV C3 H4 O6 S C(C(=O)C(=....
27 4YW9 Ki = 45 uM 1WD C6 H5 N O2 S c1cc(c(nc1....
28 3MOE Ki = 50 uM SPV C3 H4 O6 S C(C(=O)C(=....
29 2RK7 Ki = 89 uM OXL C2 O4 C(=O)(C(=O....
30 4GNM - OXL C2 O4 C(=O)(C(=O....
31 2QF1 - OAA C4 H3 O5 C(C(=O)C(=....
32 5FH2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
33 2RKA Ki = 1 mM PGA C2 H5 O6 P C(C(=O)O)O....
34 1M51 ic50 = 18.8 uM TSX C21 H25 N5 O3 CCCCN1c2c(....
35 1NHX ic50 = 2.11 uM FTB C25 H26 F N5 O3 CCCCN1c2c(....
36 4GMZ - SPV C3 H4 O6 S C(C(=O)C(=....
37 4OX2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
38 5FH0 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
39 5V97 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
40 1KHB - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
41 3DT4 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
42 2RKE Ki = 82.5 uM SAT C2 H4 O5 S C(C(=O)O)S....
43 2QEY - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
44 4YWB - OXD C2 H2 O4 C(=O)(C(=O....
45 2GMV ic50 = 0.63 uM UN8 C27 H28 F N7 O4 S CCCCN1c2c(....
46 1KHE - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
47 2QZY - PEP C3 H5 O6 P C=C(C(=O)O....
48 2FAH Ki > 50 mM MLA C3 H4 O4 C(C(=O)O)C....
50% Homology Family (49)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4R43 Kd = 9.3 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 4GMW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 4GNO - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
4 5FH1 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
5 4GNL - PEP C3 H5 O6 P C=C(C(=O)O....
6 4GNP - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 3DT2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
8 6P5O ic50 = 97 uM O2Y C8 H7 N O4 S c1cc(c(nc1....
9 5V9H - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 3MOF Ki = 860 uM OXL C2 O4 C(=O)(C(=O....
11 4GNQ - OXL C2 O4 C(=O)(C(=O....
12 2QF2 - OAA C4 H3 O5 C(C(=O)C(=....
13 4GMM - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
14 3DT7 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
15 3DTB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 5FH3 Ki = 970 uM OXL C2 O4 C(=O)(C(=O....
17 4GMU - OXL C2 O4 C(=O)(C(=O....
18 1KHF - PEP C3 H5 O6 P C=C(C(=O)O....
19 4YW8 - 1WD C6 H5 N O2 S c1cc(c(nc1....
20 4YWD - NTM C7 H5 N O4 c1cc(c(nc1....
21 5FH4 Ki = 174 uM SPV C3 H4 O6 S C(C(=O)C(=....
22 2RKD Ki = 1.9 mM 3PP C3 H7 O5 P C(CP(=O)(O....
23 3MOH Ki = 1460 uM PGA C2 H5 O6 P C(C(=O)O)O....
24 2RK8 Ki = 230 uM PPF C H3 O5 P C(=O)(O)P(....
25 5V9G Ki = 441 uM OXL C2 O4 C(=O)(C(=O....
26 5FH5 - PGA C2 H5 O6 P C(C(=O)O)O....
27 5V9F Ki = 37 uM SPV C3 H4 O6 S C(C(=O)C(=....
28 4YW9 Ki = 45 uM 1WD C6 H5 N O2 S c1cc(c(nc1....
29 3MOE Ki = 50 uM SPV C3 H4 O6 S C(C(=O)C(=....
30 2RK7 Ki = 89 uM OXL C2 O4 C(=O)(C(=O....
31 4GNM - OXL C2 O4 C(=O)(C(=O....
32 2QF1 - OAA C4 H3 O5 C(C(=O)C(=....
33 5FH2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
34 2RKA Ki = 1 mM PGA C2 H5 O6 P C(C(=O)O)O....
35 1M51 ic50 = 18.8 uM TSX C21 H25 N5 O3 CCCCN1c2c(....
36 1NHX ic50 = 2.11 uM FTB C25 H26 F N5 O3 CCCCN1c2c(....
37 4GMZ - SPV C3 H4 O6 S C(C(=O)C(=....
38 4OX2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
39 5FH0 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
40 5V97 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
41 1KHB - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
42 3DT4 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
43 2RKE Ki = 82.5 uM SAT C2 H4 O5 S C(C(=O)O)S....
44 2QEY - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
45 4YWB - OXD C2 H2 O4 C(=O)(C(=O....
46 2GMV ic50 = 0.63 uM UN8 C27 H28 F N7 O4 S CCCCN1c2c(....
47 1KHE - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
48 2QZY - PEP C3 H5 O6 P C=C(C(=O)O....
49 2FAH Ki > 50 mM MLA C3 H4 O4 C(C(=O)O)C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 3PP; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 3PP 1 1
2 Z3P 0.541667 0.666667
3 PAE 0.5 0.862069
4 KPA 0.448276 0.870968
5 PGA 0.423077 0.866667
6 GPF 0.413793 0.657895
7 DHJ 0.411765 0.705882
8 2HE 0.409091 0.75
9 CYX 0.4 0.78125
Similar Ligands (3D)
Ligand no: 1; Ligand: 3PP; Similar ligands found: 256
No: Ligand Similarity coefficient
1 X1S 0.9904
2 1GP 0.9751
3 G3P 0.9716
4 PGH 0.9626
5 PSE 0.9558
6 PPR 0.9557
7 PEP 0.9545
8 DQY 0.9534
9 G3H 0.9495
10 GZ3 0.9486
11 13P 0.9475
12 KVV 0.9462
13 4MV 0.9453
14 SIN 0.9451
15 FUM 0.9448
16 OPE 0.9435
17 H95 0.9430
18 TB6 0.9428
19 PAH 0.9425
20 A20 0.9421
21 GP9 0.9416
22 ACH 0.9416
23 S0H 0.9401
24 NMG 0.9400
25 MAE 0.9390
26 R67 0.9362
27 HX2 0.9360
28 CP 0.9355
29 PCT 0.9343
30 LMR 0.9333
31 LEU 0.9324
32 4LR 0.9318
33 1SA 0.9310
34 0V5 0.9294
35 1SH 0.9291
36 TAR 0.9286
37 LTL 0.9278
38 3SL 0.9272
39 OAA 0.9262
40 SPV 0.9261
41 SHF 0.9253
42 GLU 0.9250
43 129 0.9238
44 ASP 0.9226
45 PLU 0.9221
46 MLT 0.9200
47 URP 0.9191
48 CHH 0.9190
49 NM3 0.9180
50 COI 0.9178
51 7VD 0.9177
52 GUA 0.9175
53 9X6 0.9169
54 LLQ 0.9164
55 ICF 0.9163
56 SRT 0.9163
57 CCE 0.9157
58 KMH 0.9153
59 QMP 0.9150
60 GLN 0.9149
61 IP8 0.9147
62 PMB 0.9139
63 ASN 0.9133
64 FB2 0.9131
65 PEQ 0.9130
66 PRO 0.9106
67 DGN 0.9105
68 PPV 0.9101
69 HDA 0.9101
70 OKG 0.9100
71 TLA 0.9099
72 9ON 0.9098
73 CMS 0.9083
74 UGC 0.9081
75 3PG 0.9079
76 CCD 0.9078
77 IOM 0.9077
78 PIS 0.9075
79 TEO 0.9069
80 1DQ 0.9069
81 DAS 0.9065
82 OEG 0.9062
83 ONL 0.9059
84 ZGL 0.9057
85 CRN 0.9057
86 THE 0.9054
87 AKG 0.9053
88 POA 0.9053
89 2IT 0.9051
90 MPD 0.9049
91 SEP 0.9047
92 8K2 0.9045
93 40E 0.9044
94 DGL 0.9042
95 SPA 0.9042
96 2HG 0.9036
97 GPJ 0.9025
98 2AS 0.9023
99 GLY GLY 0.9021
100 2PN 0.9019
101 S2G 0.9015
102 EHM 0.9015
103 2RH 0.9010
104 NM2 0.9009
105 98J 0.9006
106 VKC 0.9005
107 NXA 0.9004
108 AL0 0.8998
109 HG3 0.8990
110 UY7 0.8987
111 B85 0.8984
112 CHT 0.8981
113 POP 0.8980
114 DAV 0.8974
115 IZC 0.8971
116 SHO 0.8970
117 ITN 0.8963
118 HSO 0.8960
119 HYP 0.8959
120 6NA 0.8953
121 XUL 0.8949
122 MEQ 0.8949
123 PC 0.8942
124 8X3 0.8939
125 HSE 0.8934
126 69O 0.8932
127 P7I 0.8931
128 6PC 0.8928
129 NLE 0.8927
130 3S5 0.8927
131 TAU 0.8926
132 LEA 0.8923
133 HTX 0.8922
134 ABU 0.8919
135 0VT 0.8918
136 AHB 0.8917
137 KVP 0.8913
138 3LR 0.8910
139 RTK 0.8909
140 BEN 0.8902
141 AT3 0.8901
142 152 0.8891
143 ORN 0.8890
144 OK7 0.8888
145 NIO 0.8887
146 MDN 0.8887
147 COM 0.8885
148 1DV 0.8872
149 URQ 0.8872
150 2CO 0.8869
151 PAC 0.8868
152 BEZ 0.8865
153 5FX 0.8860
154 DYA 0.8860
155 EOU 0.8849
156 PRS 0.8847
157 SAN 0.8844
158 PG3 0.8833
159 49F 0.8833
160 NCA 0.8832
161 JYD 0.8832
162 IHG 0.8828
163 RUJ 0.8825
164 ETM 0.8824
165 SSN 0.8819
166 HSM 0.8813
167 TSU 0.8812
168 7WG 0.8811
169 RSO 0.8810
170 HIS 0.8808
171 OGA 0.8807
172 HPV 0.8806
173 K34 0.8804
174 XLS 0.8804
175 TPA 0.8798
176 M6W 0.8795
177 HGA 0.8792
178 HL5 0.8792
179 2FT 0.8790
180 MET 0.8789
181 YCP 0.8786
182 DE5 0.8784
183 A09 0.8784
184 DS0 0.8781
185 IXW 0.8780
186 449 0.8779
187 AMS 0.8776
188 ISZ 0.8774
189 ZBT 0.8774
190 CFI 0.8772
191 7BC 0.8769
192 FOC 0.8766
193 URS 0.8764
194 4J8 0.8757
195 TZL 0.8753
196 HIO 0.8750
197 X1R 0.8749
198 UNU 0.8747
199 FBS 0.8743
200 1DU 0.8738
201 QY9 0.8735
202 JZ5 0.8734
203 HBU 0.8733
204 VAH 0.8731
205 PBC 0.8727
206 DHI 0.8722
207 HPS 0.8721
208 AAS 0.8721
209 AG2 0.8716
210 2PG 0.8715
211 MED 0.8713
212 BUB 0.8713
213 MUC 0.8706
214 LYS 0.8706
215 0OC 0.8703
216 SD4 0.8688
217 FBJ 0.8686
218 EFS 0.8684
219 RMN 0.8683
220 PMF 0.8682
221 GRO 0.8679
222 9SB 0.8677
223 NIZ 0.8677
224 LNO 0.8666
225 C21 0.8665
226 URO 0.8664
227 PHU 0.8663
228 BNS 0.8663
229 FCR 0.8662
230 3YP 0.8661
231 FQI 0.8654
232 16D 0.8644
233 FBW 0.8643
234 XPO 0.8634
235 9YL 0.8634
236 BHH 0.8633
237 MEV 0.8627
238 K6H 0.8627
239 XBT 0.8625
240 MZT 0.8625
241 A8C 0.8625
242 HYA 0.8623
243 RBL 0.8619
244 DHM 0.8612
245 GJZ 0.8611
246 M4T 0.8601
247 DHS 0.8600
248 LYN 0.8598
249 3QM 0.8592
250 9J3 0.8588
251 1SP 0.8585
252 S8V 0.8577
253 RAT 0.8568
254 GWM 0.8567
255 FEH 0.8544
256 2EH 0.8544
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1NHX; Ligand: FTB; 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: 1nhx.bio1) has 44 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1NHX; Ligand: PEP; 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: 1nhx.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
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