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(...
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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 10 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 (51)
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 4UOG - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
40 4UOH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
41 2AZ3 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
42 1NHK - CMP C10 H12 N5 O6 P c1nc(c2c(n....
43 1NLK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
44 1BE4 - PCG C10 H12 N5 O7 P c1nc2c(n1[....
45 3BBB - DG C10 H14 N5 O7 P c1nc2c(n1[....
46 1NUE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
47 1BHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
48 2HVD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
49 1UCN Kd = 6 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50 3BBF - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
51 2HVE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CMP; Similar ligands found: 94
No: Ligand ECFP6 Tc MDL keys Tc
1 CMP 1 1
2 2BA 1 0.984848
3 SP1 0.757143 0.928571
4 RP1 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 C2E 0.534091 0.902778
16 35G 0.534091 0.888889
17 PCG 0.534091 0.888889
18 1YC 0.53 0.875
19 Y3J 0.506667 0.753623
20 5CD 0.5 0.811594
21 XYA 0.5 0.826087
22 ACK 0.5 0.897059
23 ADN 0.5 0.826087
24 RAB 0.5 0.826087
25 6SW 0.494382 0.9
26 5AD 0.493151 0.776119
27 5N5 0.486842 0.8
28 75G 0.483146 0.890411
29 A4D 0.480519 0.8
30 M2T 0.475 0.736842
31 MTA 0.469136 0.777778
32 CC5 0.466667 0.850746
33 EP4 0.4625 0.756757
34 DTA 0.45679 0.816901
35 QQX 0.452381 0.835616
36 AMP 0.447059 0.927536
37 A 0.447059 0.927536
38 QQY 0.447059 0.847222
39 3DH 0.440476 0.777778
40 AMP MG 0.436782 0.875
41 3AM 0.435294 0.913043
42 ABM 0.431818 0.901408
43 J7C 0.431818 0.75
44 A2D 0.431818 0.928571
45 ZAS 0.430233 0.77027
46 7D7 0.428571 0.771429
47 S4M 0.426966 0.666667
48 6RE 0.425287 0.74026
49 SRA 0.425287 0.876712
50 3AD 0.425 0.838235
51 2AM 0.423529 0.9
52 AP2 0.422222 0.864865
53 A12 0.422222 0.864865
54 BA3 0.422222 0.928571
55 MAO 0.422222 0.740741
56 NEC 0.420455 0.726027
57 A3G 0.420455 0.780822
58 DSH 0.420455 0.727273
59 AOC 0.420455 0.802817
60 BEF ADP 0.419355 0.84
61 SFG 0.419355 0.753425
62 ADP BEF 0.419355 0.84
63 6JR 0.419048 0.927536
64 B4P 0.417582 0.928571
65 5AS 0.417582 0.741176
66 AP5 0.417582 0.928571
67 ADP 0.417582 0.901408
68 A3N 0.41573 0.767123
69 APC 0.414894 0.864865
70 SON 0.413043 0.864865
71 AN2 0.413043 0.888889
72 EEM 0.412371 0.691358
73 GJV 0.411111 0.730769
74 GGZ 0.41 0.78481
75 OVE 0.409091 0.863014
76 ADP MG 0.408602 0.863014
77 AU1 0.408602 0.876712
78 M33 0.408602 0.888889
79 CA0 0.408602 0.876712
80 ADX 0.408602 0.810127
81 A3P 0.406593 0.927536
82 5X8 0.404255 0.767123
83 50T 0.404255 0.888889
84 ATP 0.404255 0.901408
85 ACP 0.404255 0.876712
86 VO4 ADP 0.40404 0.888889
87 ADP VO4 0.40404 0.888889
88 SAM 0.402062 0.691358
89 0UM 0.401961 0.7
90 AQP 0.4 0.901408
91 APR 0.4 0.901408
92 PRX 0.4 0.876712
93 AR6 0.4 0.901408
94 5FA 0.4 0.901408
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1NHK; Ligand: CMP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1NHK; Ligand: CMP; Similar sites found: 164
This union binding pocket(no: 2) in the query (biounit: 1nhk.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3CBG 4FE 0.005899 0.4655 None
2 4JCA CIT 0.006606 0.46282 None
3 3MAG 3MA 0.00927 0.45482 None
4 2WGC SIA GAL BGC 0.0201 0.44471 None
5 1BTN I3P 0.03348 0.4402 None
6 2X2T GAL NGA 0.01372 0.43789 None
7 1JGS SAL 0.02677 0.43755 None
8 1UO4 PIH 0.01963 0.43703 None
9 1O9U ADZ 0.01437 0.43683 None
10 1UO5 PIH 0.03074 0.4341 None
11 1EYE PMM 0.003307 0.42115 None
12 1G8S MET 0.01449 0.41808 None
13 2QCX PF1 0.01359 0.41417 None
14 1TUV VK3 0.04199 0.41232 None
15 1Q3P GLU ALA GLN THR ARG LEU 0.009598 0.41126 None
16 1QD0 RR6 0.009557 0.40282 None
17 4IXW IXW 0.01602 0.40184 None
18 2BZ1 TAU 0.00392 0.48523 1.38889
19 2XI7 XI7 0.009218 0.46407 1.38889
20 1HFA PIO 0.003451 0.41813 1.38889
21 1H8P PC 0.01965 0.42971 1.83486
22 2XRH NIO 0.01674 0.42067 2
23 3ZGE ASP 0.001052 0.48683 2.08333
24 3O03 GCO 0.009363 0.44655 2.08333
25 1XX4 BAM 0.009742 0.44565 2.08333
26 1JN2 SFP 0.01941 0.42779 2.08333
27 2JFV FLC 0.00922 0.42724 2.08333
28 2EB5 OXL 0.01844 0.41319 2.08333
29 1SQ5 PAU 0.02137 0.40075 2.08333
30 1SC3 MLI 0.01212 0.43374 2.27273
31 2BOI MFU 0.01996 0.40205 2.65487
32 1Z42 HBA 0.01505 0.45643 2.77778
33 2FGQ MLT 0.01276 0.42067 2.77778
34 1GU3 BGC BGC BGC BGC BGC 0.007963 0.41948 2.77778
35 2Q1A 2KT 0.01614 0.41589 2.77778
36 3U1T MLI 0.003456 0.45373 3.47222
37 3P3N AKG 0.004832 0.4403 3.47222
38 2Y7P SAL 0.003462 0.43522 3.47222
39 2DWU DGL 0.003893 0.42779 3.47222
40 1H2M OGA 0.01055 0.42451 3.47222
41 2XUM OGA 0.01166 0.42249 3.47222
42 1H2K OGA 0.01788 0.41382 3.47222
43 1WRA PC 0.0333 0.40613 3.47222
44 2Y0I AKG 0.0232 0.40367 3.47222
45 4B7E OGA 0.02461 0.40251 3.47222
46 2QGI UDP 0.0254 0.40188 3.47222
47 2QLX RM4 0.01865 0.41839 3.7037
48 4W6Z ETF 0.002345 0.47785 4.16667
49 1Y9Q MED 0.003502 0.4468 4.16667
50 1SS4 GSH 0.02992 0.43846 4.16667
51 1Y7P RIP 0.01898 0.42394 4.16667
52 2HW1 FRU 0.01041 0.4194 4.16667
53 1W3R PYR 0.03635 0.40967 4.16667
54 3SHR CMP 0.008924 0.40817 4.16667
55 4N7C AEF 0.03399 0.40569 4.16667
56 4CCO OGA 0.0166 0.40556 4.16667
57 4B9E FAH 0.001428 0.4722 4.86111
58 1I0Z OXM 0.005702 0.45778 4.86111
59 1RZM E4P 0.004422 0.44857 4.86111
60 3HZL 6PC 0.01099 0.44291 4.86111
61 2Q3M MLA 0.01122 0.44245 4.86111
62 4BT5 23B 0.002599 0.43519 4.86111
63 4JLV ADP 0.04423 0.42115 4.86111
64 2YIV YIV 0.02323 0.41952 4.86111
65 2Q8H TF4 0.03327 0.41768 4.86111
66 1FBL HTA 0.006753 0.41312 4.86111
67 4CIB 7UZ 0.01717 0.40959 4.86111
68 3CEV ARG 0.01206 0.40707 4.86111
69 3CL5 SIO 0.03342 0.40605 4.86111
70 2YD6 FLC 0.04286 0.40589 4.86111
71 1A59 CIT 0.03541 0.40483 4.86111
72 3JQM GTP 0.01763 0.40008 4.86111
73 2BO4 FLC 0.04439 0.40001 4.86111
74 2OFD NGA 0.001062 0.47085 4.92958
75 2OFE NAG 0.001152 0.46922 4.92958
76 4RJK PYR 0.002854 0.49307 5.55556
77 3IHB TRS 0.005078 0.46932 5.55556
78 4LIT AKG 0.002285 0.449 5.55556
79 5EQU AKG 0.01213 0.43372 5.55556
80 2VQ5 LDP 0.02952 0.42042 5.55556
81 1QH9 LAC 0.01757 0.41417 5.55556
82 2VQ5 HBA 0.02508 0.41213 5.55556
83 3S9K CIT 0.02971 0.42436 5.9322
84 1NU4 MLA 0.009019 0.46461 6.18557
85 1YOE RIB 0.0002031 0.48177 6.25
86 2ZWS PLM 0.01972 0.44518 6.25
87 1GJW GLC 0.005228 0.44507 6.25
88 2GWD GLU 0.01003 0.41045 6.25
89 1Y13 BIO 0.01068 0.40497 6.25
90 1FP2 SAH 0.008149 0.40161 6.25
91 1C3V PDC 0.02624 0.40125 6.25
92 3U7Y FLC 0.02607 0.44269 6.94444
93 1NXJ GLV 0.01438 0.40383 6.94444
94 4B16 NAG 0.004347 0.47271 7.63889
95 2IZ1 ATR 0.01156 0.42265 7.63889
96 2NVK NAP 0.01031 0.41459 7.63889
97 3AYS CT3 0.009482 0.40709 7.63889
98 3P7I P7I 0.01627 0.40594 7.63889
99 3WUD GLC GAL 0.02097 0.42177 8.08823
100 1JAC AMG 0.01643 0.44126 8.27068
101 4M5P MLA 0.002016 0.49082 8.33333
102 2VDJ HSE 0.002507 0.46799 8.33333
103 4O8A 2OP 0.02219 0.42694 8.33333
104 1QO0 BMD 0.01414 0.41858 8.33333
105 1V6A TRE 0.01463 0.41273 8.33333
106 1H8G CHT 0.008178 0.46704 8.42105
107 2XDQ MGX 0.003177 0.471 9.02778
108 1T0S BML 0.002976 0.46427 9.02778
109 1ZUW DGL 0.001316 0.44762 9.02778
110 1DXY COI 0.01015 0.44472 9.02778
111 1ZGA HMK 0.003672 0.41934 9.02778
112 1ULE GLA GAL NAG 0.0317 0.41269 9.02778
113 4EXO PYR 0.03622 0.40975 9.02778
114 4G09 0VD 0.003998 0.40949 9.02778
115 3RKR NAP 0.008624 0.40877 9.02778
116 1R5A GTS 0.01525 0.40275 9.02778
117 1H16 PYR 0.002031 0.47256 9.72222
118 1NF8 BOG 0.02727 0.41546 9.72222
119 1I0B PEL 0.02893 0.41204 9.72222
120 1H16 DTL 0.0439 0.41129 9.72222
121 1KC7 PPR 0.03583 0.40458 9.72222
122 1YOA FMN 0.02571 0.43857 10.0629
123 4WBD CIT 0.003311 0.46196 10.4167
124 3VCA PRO 0.002834 0.44185 10.4167
125 1P72 THM 0.00621 0.42418 10.4167
126 4WBD ADP 0.02358 0.41344 10.4167
127 2I4O ATP 0.01268 0.4019 10.4167
128 2ZJ5 ADP 0.02764 0.40022 10.4167
129 3TKA CTN 0.0001399 0.57409 11.1111
130 3NNF AKG 0.004681 0.44094 11.1111
131 1P9B HDA 0.008371 0.42366 11.1111
132 3SCH TB6 0.02534 0.40672 11.1111
133 1UW1 ADP 0.01845 0.40817 11.25
134 2WCV FUC 0.001591 0.4388 11.4286
135 2JC9 ADN 0.01363 0.40931 11.8056
136 4Q3F TLA 0.005733 0.43685 11.9658
137 1Y2W NAG 0.003683 0.44578 11.9718
138 3R51 MMA 0.0181 0.43158 12.5
139 1GPJ CIT 0.0209 0.41064 12.5
140 1OIK AKG 0.02905 0.40392 12.5
141 3BHO B4P 0.02116 0.43524 13.1944
142 3I7S PYR 0.007188 0.44512 13.8889
143 3F81 STT 0.04085 0.41296 13.8889
144 2C5S AMP 0.01568 0.40224 13.8889
145 1Z45 GAL 0.006602 0.42303 14.5833
146 4M51 BEZ 0.01249 0.43309 15.2778
147 3L24 GOA 0.01971 0.42964 15.2778
148 3GM5 CIT 0.02557 0.40653 15.2778
149 3MA0 XYP 0.04469 0.40014 15.9722
150 3QDV NDG 0.0006542 0.4885 16.7832
151 3QDY CBS 0.0008298 0.48353 16.7832
152 3QDW NDG 0.001008 0.47947 16.7832
153 3QDY A2G GAL 0.003074 0.46357 16.7832
154 3QDV A2G 0.005393 0.45904 16.7832
155 3QDT A2G GAL 0.03565 0.4101 16.7832
156 2V5E SCR 0.04835 0.41546 16.8317
157 4CCN OGA 0.009454 0.42673 17.1429
158 2Z9V PXM 0.003272 0.43629 17.3611
159 2CW6 3HG 0.01262 0.43978 18.0556
160 9LDT OXM 0.03779 0.42139 20.8333
161 9LDB OXM 0.04164 0.41906 20.8333
162 4HA6 PXM 0.01498 0.41226 22.9167
163 4QVH FLC 0.013 0.45911 24.3056
164 3UBW 6SP 0.007962 0.45752 42.8571
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