Receptor
PDB id Resolution Class Description Source Keywords
1NHK 1.9 Å EC: 2.7.4.6 CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE S UBSTRATE AT 2.0 ANGSTROMS RESOLUTION MYXOCOCCUS XANTHUS PHOSPHOTRANSFERASE
Ref.: THE 1.9 A CRYSTAL STRUCTURE OF A NUCLEOSIDE DIPHOSPHATE KINASE COMPLEX WITH ADENOSINE 3',5'-CYCLIC MONOPHOSPHATE: EVIDENCE FOR COMPETITIVE INHIBITION. J.MOL.BIOL. V. 249 665 1995
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CMP L:146;
R:1;
Valid;
Valid;
none;
none;
submit data
329.206 C10 H12 N5 O6 P c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1NHK 1.9 Å EC: 2.7.4.6 CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE S UBSTRATE AT 2.0 ANGSTROMS RESOLUTION MYXOCOCCUS XANTHUS PHOSPHOTRANSFERASE
Ref.: THE 1.9 A CRYSTAL STRUCTURE OF A NUCLEOSIDE DIPHOSPHATE KINASE COMPLEX WITH ADENOSINE 3',5'-CYCLIC MONOPHOSPHATE: EVIDENCE FOR COMPETITIVE INHIBITION. J.MOL.BIOL. V. 249 665 1995
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 1NHK - CMP C10 H12 N5 O6 P c1nc(c2c(n....
2 1NLK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1NHK - CMP C10 H12 N5 O6 P c1nc(c2c(n....
2 1NLK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50% Homology Family (57)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1F6T - TBD C10 H19 B N2 O10 P2 [BH3-][P@@....
2 1NDP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 3FKB - TNM C9 H15 N5 O7 P2 C[C@H](Cn1....
4 1KDN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
5 1LWX - AZD C10 H15 N5 O10 P2 CC1=CN(C(=....
6 1NDC - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
7 2BEF - BEF ADP n/a n/a
8 1F3F Kd = 21.3 uM D4T C10 H15 N2 O13 P3 CC1=CN(C(=....
9 4CP5 Kd = 452 uM EOI C9 H16 N5 O9 P3 S C[C@H](Cn1....
10 1B4S - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 1S5Z - SON C12 H16 N5 O8 P c1nc(c2c(n....
12 1MN7 - ABT C10 H17 B N5 O12 P3 B=P(O)(OC[....
13 3EVO - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
14 3ELH - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
15 3GP9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 3EJM - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
17 3FBB - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
18 3EMT - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
19 3FCV - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
20 3EIC - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
21 3EVM - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
22 3B6B - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
23 3FCW - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
24 2B8Q - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
25 3DKD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
26 3DDI - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
27 3FBE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
28 3ETM - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
29 3GPA - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
30 3ENA - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
31 3EM1 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
32 3EE3 - CDP MG n/a n/a
33 3NGU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
34 3Q86 - GTP MG n/a n/a
35 3Q8U - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
36 3Q8V - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
37 1WKL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
38 1ZS6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
39 6XPV - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
40 6XPW - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
41 6XPU - IDP C10 H14 N4 O11 P2 c1nc2c(n1[....
42 6XPT - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
43 6XP7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
44 6XPS - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
45 4UOG - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
46 4UOH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
47 2AZ3 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
48 1NHK - CMP C10 H12 N5 O6 P c1nc(c2c(n....
49 1NLK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50 1BE4 - PCG C10 H12 N5 O7 P c1nc2c(n1[....
51 3BBB - DG C10 H14 N5 O7 P c1nc2c(n1[....
52 1NUE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
53 1BHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
54 2HVD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
55 1UCN Kd = 6 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
56 3BBF - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
57 2HVE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: CMP; Similar ligands found: 106
No: Ligand ECFP6 Tc MDL keys Tc
1 2BA 1 0.984848
2 CMP 1 1
3 RP1 0.757143 0.928571
4 SP1 0.757143 0.928571
5 1YD 0.727273 0.902778
6 4BW 0.727273 0.902778
7 1SY 0.653061 0.902778
8 1OR 0.635294 0.807692
9 4UR 0.626263 0.902778
10 7CH 0.580247 0.984615
11 6SX 0.573171 0.953846
12 6SZ 0.559524 0.984848
13 N6S 0.535354 0.914286
14 N6R 0.535354 0.914286
15 PCG 0.534091 0.888889
16 35G 0.534091 0.888889
17 C2E 0.534091 0.902778
18 1YC 0.53 0.875
19 AF2 AF2 AF2 AF2 AF2 AF2 0.517647 0.84507
20 Y3J 0.506667 0.753623
21 RAB 0.5 0.826087
22 5CD 0.5 0.811594
23 ADN 0.5 0.826087
24 ACK 0.5 0.897059
25 XYA 0.5 0.826087
26 6SW 0.494382 0.9
27 5AD 0.493151 0.776119
28 5N5 0.486842 0.8
29 75G 0.483146 0.890411
30 A4D 0.480519 0.8
31 NWW 0.480519 0.764706
32 M2T 0.475 0.736842
33 MTA 0.469136 0.777778
34 CC5 0.466667 0.850746
35 EP4 0.4625 0.756757
36 DTA 0.45679 0.816901
37 QQX 0.452381 0.835616
38 A 0.447059 0.927536
39 QQY 0.447059 0.847222
40 AMP 0.447059 0.927536
41 LMS 0.447059 0.7875
42 AMP MG 0.44186 0.913043
43 3DH 0.440476 0.777778
44 NWQ 0.440476 0.742857
45 N5O 0.436782 0.743243
46 3AM 0.435294 0.913043
47 KT2 0.434783 0.902778
48 45A 0.431818 0.901408
49 A2D 0.431818 0.928571
50 J7C 0.431818 0.75
51 ABM 0.431818 0.901408
52 ZAS 0.430233 0.77027
53 7D7 0.428571 0.771429
54 S4M 0.426966 0.666667
55 SRA 0.425287 0.876712
56 6RE 0.425287 0.74026
57 3AD 0.425 0.838235
58 2AM 0.423529 0.9
59 A12 0.422222 0.864865
60 AP2 0.422222 0.864865
61 MAO 0.422222 0.740741
62 BA3 0.422222 0.928571
63 DSH 0.420455 0.727273
64 A3G 0.420455 0.780822
65 NEC 0.420455 0.726027
66 AOC 0.420455 0.802817
67 OZV 0.42 0.901408
68 SFG 0.419355 0.753425
69 6JR 0.419048 0.927536
70 ADP 0.417582 0.901408
71 AP5 0.417582 0.928571
72 B4P 0.417582 0.928571
73 5AS 0.417582 0.741176
74 KL2 0.416667 0.84507
75 A3N 0.41573 0.767123
76 APC 0.414894 0.864865
77 AN2 0.413043 0.888889
78 SON 0.413043 0.864865
79 AT4 0.413043 0.864865
80 ADP MG 0.413043 0.9
81 ADP BEF 0.413043 0.9
82 EEM 0.412371 0.691358
83 LQJ 0.411215 0.928571
84 GJV 0.411111 0.730769
85 N5A 0.411111 0.716216
86 GGZ 0.41 0.78481
87 OVE 0.409091 0.863014
88 AU1 0.408602 0.876712
89 CA0 0.408602 0.876712
90 ADX 0.408602 0.810127
91 M33 0.408602 0.888889
92 A3P 0.406593 0.927536
93 ACP 0.404255 0.876712
94 5X8 0.404255 0.767123
95 KG4 0.404255 0.876712
96 ATP 0.404255 0.901408
97 50T 0.404255 0.888889
98 HEJ 0.404255 0.901408
99 SAM 0.402062 0.691358
100 0UM 0.401961 0.7
101 NWZ 0.4 0.727273
102 AR6 0.4 0.901408
103 AQP 0.4 0.901408
104 5FA 0.4 0.901408
105 APR 0.4 0.901408
106 PRX 0.4 0.876712
Similar Ligands (3D)
Ligand no: 1; Ligand: CMP; Similar ligands found: 267
No: Ligand Similarity coefficient
1 6J7 0.9695
2 6SY 0.9537
3 5GP 0.9481
4 CC7 0.9475
5 7D5 0.9238
6 3GP 0.9217
7 D5M 0.9200
8 DGP 0.9164
9 IMH 0.9147
10 0QX 0.9126
11 8BR 0.9121
12 DBM 0.9110
13 QRP 0.9082
14 QTJ 0.9071
15 FMC 0.9063
16 UFP 0.9061
17 C4F 0.9050
18 TMP 0.9048
19 NYM 0.9046
20 IGP 0.9044
21 1DA 0.9041
22 C5Q 0.9041
23 AFX 0.9036
24 NOS 0.9036
25 IMP 0.9032
26 TBN 0.9032
27 LRT 0.9020
28 8MF 0.9014
29 HMK 0.9011
30 G 0.9005
31 CH 0.9002
32 5R9 0.9000
33 71V 0.8995
34 FDM 0.8989
35 4YE 0.8986
36 FEU 0.8983
37 LFK 0.8982
38 2DT 0.8980
39 MQR 0.8979
40 LOX XYP 0.8978
41 TCT 0.8972
42 9W8 0.8970
43 5FD 0.8967
44 AGV 0.8966
45 EST 0.8965
46 5CK 0.8961
47 UMP 0.8957
48 DU 0.8957
49 U 0.8957
50 CWU 0.8949
51 MTP 0.8945
52 U5P 0.8944
53 GMP 0.8941
54 9RK 0.8939
55 94M 0.8938
56 8OG 0.8936
57 DCM 0.8935
58 XYP XYS 0.8930
59 JMQ 0.8929
60 FTU 0.8928
61 KTM 0.8919
62 VIB 0.8917
63 XYP XYP 0.8917
64 MBY 0.8914
65 1OX 0.8911
66 KUP 0.8907
67 P1Y 0.8903
68 IXG 0.8900
69 HPR 0.8895
70 PRH 0.8895
71 HFS 0.8894
72 CHJ 0.8893
73 5F1 0.8891
74 ECS 0.8890
75 SDN 0.8889
76 MDR 0.8889
77 5ID 0.8885
78 DDN 0.8883
79 0NH 0.8880
80 M77 0.8879
81 C 0.8878
82 NXB 0.8877
83 205 0.8869
84 XYP XIM 0.8868
85 4K2 0.8868
86 QNI 0.8867
87 SIJ 0.8866
88 103 0.8865
89 Q11 0.8861
90 9KL 0.8859
91 JA3 0.8857
92 IMK 0.8856
93 ACJ 0.8854
94 FT3 0.8851
95 C5P 0.8849
96 ESZ 0.8846
97 DOC 0.8841
98 8CS 0.8841
99 XYS XYS 0.8839
100 7CS 0.8835
101 MQ1 0.8833
102 PUR 0.8832
103 27M 0.8828
104 FMP 0.8825
105 CR4 0.8823
106 BMZ 0.8823
107 5CJ 0.8821
108 69K 0.8820
109 15I 0.8819
110 ON1 0.8818
111 5HU 0.8816
112 EQU 0.8816
113 J90 0.8815
114 7G0 0.8811
115 1V8 0.8810
116 7XX 0.8805
117 801 0.8805
118 CDY 0.8799
119 FB4 0.8799
120 WCU 0.8797
121 UMC 0.8796
122 SCE 0.8796
123 QEI 0.8794
124 PV0 0.8794
125 120 0.8793
126 7FZ 0.8792
127 QS4 0.8789
128 ESL 0.8785
129 CHV 0.8784
130 7G1 0.8783
131 IXE 0.8781
132 L6Y 0.8781
133 47X 0.8780
134 P1S 0.8777
135 F91 0.8773
136 4KN 0.8771
137 7ZO 0.8768
138 J3Z 0.8766
139 TXS 0.8765
140 NVS 0.8765
141 FT2 0.8764
142 ZT2 0.8761
143 TQT 0.8757
144 TYP 0.8755
145 4P9 0.8750
146 5F7 0.8748
147 CQW 0.8748
148 EZB 0.8743
149 5YA 0.8742
150 INI 0.8739
151 KTV 0.8734
152 TKT 0.8728
153 CWE 0.8727
154 JFS 0.8726
155 72H 0.8725
156 4NR 0.8722
157 Q0K 0.8721
158 GEN 0.8720
159 3WJ 0.8720
160 PFT 0.8711
161 TOP 0.8711
162 TCL 0.8710
163 FTK 0.8707
164 NOJ BGC 0.8706
165 6WR 0.8704
166 15Q 0.8704
167 IQW 0.8702
168 QTM 0.8700
169 MR4 0.8699
170 GJB 0.8699
171 ESM 0.8698
172 B2L 0.8698
173 1Q4 0.8697
174 8M5 0.8697
175 GJW 0.8696
176 F01 0.8693
177 4L2 0.8693
178 CBJ 0.8692
179 Q92 0.8692
180 AOM 0.8691
181 6QT 0.8686
182 17M 0.8683
183 PV2 0.8681
184 6EL 0.8676
185 6BK 0.8670
186 MCF 0.8670
187 FT1 0.8669
188 PV1 0.8667
189 JZ8 0.8666
190 J43 0.8663
191 QTV 0.8662
192 3WK 0.8661
193 XDL XYP 0.8661
194 EMU 0.8658
195 KWV 0.8654
196 6WL 0.8654
197 MRE 0.8653
198 68C 0.8652
199 D59 0.8651
200 AJ6 0.8647
201 8WB 0.8645
202 7G2 0.8643
203 MI2 0.8640
204 M01 0.8636
205 AX6 0.8635
206 PV8 0.8634
207 MR5 0.8633
208 RE2 0.8621
209 J5Z 0.8620
210 T98 0.8619
211 GZT 0.8618
212 ZTW 0.8617
213 1UR 0.8613
214 BRY 0.8612
215 LU2 0.8607
216 PZJ 0.8606
217 72E 0.8606
218 JPB 0.8605
219 B5A 0.8602
220 124 0.8602
221 CUE 0.8602
222 2BI 0.8599
223 EF2 0.8599
224 IXM 0.8596
225 YUG 0.8596
226 GAL FUC 0.8595
227 JOE 0.8595
228 AJ8 0.8592
229 2QV 0.8591
230 WDT 0.8591
231 LVY 0.8590
232 XYS AZI XYS 0.8590
233 URI 0.8589
234 CC2 0.8588
235 51P 0.8588
236 0DJ 0.8583
237 7A9 0.8583
238 DTC 0.8581
239 2QU 0.8581
240 NEU 0.8580
241 TVC 0.8580
242 8HG 0.8580
243 CX5 0.8580
244 OJ7 0.8576
245 1CE 0.8575
246 29F 0.8574
247 AP6 0.8571
248 TQ4 0.8566
249 DHT 0.8565
250 6ZE 0.8559
251 IMQ 0.8558
252 BFS 0.8556
253 XDI 0.8553
254 1V0 0.8552
255 789 0.8551
256 OAG 0.8549
257 1HP 0.8547
258 738 0.8544
259 OSY 0.8544
260 NQE 0.8539
261 2H4 0.8538
262 CUH 0.8536
263 A64 0.8529
264 E2N 0.8522
265 F21 0.8522
266 9HK 0.8521
267 SJR 0.8521
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1NHK; Ligand: CMP; 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: 1nhk.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1NHK; Ligand: CMP; 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: 1nhk.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1NHK; Ligand: CMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1nhk.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1NHK; Ligand: CMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1nhk.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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