Receptor
PDB id Resolution Class Description Source Keywords
1I52 1.5 Å EC: 2.7.7.- CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOB IOSYNTHESIS ESCHERICHIA COLI CYTIDYLYLTRANSFERASE DEOXYXYLULOSE-5-PHOSPHATE PATHWAY (DXPISOPRENOID BIOSYNTHESYS MEP TRANSFERASE
Ref.: STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C- METHYLERYTHRIT SYNTHETASE INVOLVED IN MEVALONATE- INDEPENDENT ISOP BIOSYNTHESIS. NAT.STRUCT.BIOL. V. 8 641 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:2001;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
CTP A:1001;
Valid;
none;
submit data
483.156 C9 H16 N3 O14 P3 C1=CN...
MG A:2002;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1I52 1.5 Å EC: 2.7.7.- CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOB IOSYNTHESIS ESCHERICHIA COLI CYTIDYLYLTRANSFERASE DEOXYXYLULOSE-5-PHOSPHATE PATHWAY (DXPISOPRENOID BIOSYNTHESYS MEP TRANSFERASE
Ref.: STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C- METHYLERYTHRIT SYNTHETASE INVOLVED IN MEVALONATE- INDEPENDENT ISOP BIOSYNTHESIS. NAT.STRUCT.BIOL. V. 8 641 2001
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 1I52 - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
2 1INI - CDM C14 H25 N3 O14 P2 C[C@](CO)(....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 1I52 - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
2 1INI - CDM C14 H25 N3 O14 P2 C[C@](CO)(....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 1I52 - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
2 1INI - CDM C14 H25 N3 O14 P2 C[C@](CO)(....
3 2XWL - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
4 2XWM - C5P C9 H14 N3 O8 P C1=CN(C(=O....
5 4NAL ic50 = 2.2 uM H70 C10 H4 Br3 Cl2 N O c1c(cc(c(c....
6 5MRO ic50 = 2 uM Q9P C12 H9 Cl N4 O c1ccc(cc1)....
7 5HS2 - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CTP; Similar ligands found: 83
No: Ligand ECFP6 Tc MDL keys Tc
1 CTP 1 1
2 CDP 0.895522 1
3 CAR 0.753623 0.985507
4 C 0.753623 0.985507
5 C5P 0.753623 0.985507
6 7XL 0.74026 0.944444
7 C2G 0.734177 0.957747
8 C5G 0.702381 0.944444
9 CDM 0.690476 0.894737
10 CDC 0.678571 0.82716
11 CXY 0.674419 0.944444
12 CDP MG 0.662338 0.90411
13 UTP 0.620253 0.942029
14 1AA 0.617021 0.906667
15 DCP 0.609756 0.90411
16 CTN 0.608696 0.857143
17 AR3 0.608696 0.857143
18 91P 0.582524 0.851852
19 I5A 0.577465 0.816901
20 C C 0.568182 0.929577
21 UDP 0.54321 0.942029
22 2AA 0.542056 0.693878
23 MCN 0.542056 0.819277
24 C3P 0.538462 0.942857
25 YYY 0.52381 0.90411
26 PMT 0.52381 0.85
27 GCQ 0.523256 0.90411
28 CSQ 0.520408 0.905405
29 CSV 0.520408 0.905405
30 16B 0.518519 0.917808
31 PCD 0.517544 0.781609
32 C2P 0.5 0.957143
33 GPC 0.495575 0.819277
34 FN5 0.495413 0.871795
35 CSF 0.491071 0.871795
36 DKZ 0.481013 0.746667
37 8GT 0.473118 0.907895
38 UNP 0.47191 0.915493
39 TKW 0.46988 0.971429
40 H6Y 0.463158 0.855263
41 5HM 0.458824 0.958333
42 G C 0.45614 0.8375
43 MGT 0.453608 0.829268
44 UDH 0.452632 0.844156
45 UPP 0.452632 0.888889
46 UFM 0.447917 0.888889
47 GDU 0.447917 0.888889
48 GUD 0.447917 0.888889
49 UPG 0.447917 0.888889
50 DCM 0.447059 0.890411
51 DC 0.447059 0.890411
52 UFG 0.434343 0.842105
53 U2F 0.434343 0.842105
54 UPF 0.434343 0.842105
55 U5P 0.433735 0.927536
56 URM 0.43299 0.876712
57 660 0.43299 0.876712
58 UP5 0.432432 0.857143
59 5GW 0.431579 0.890411
60 UPU 0.430108 0.887324
61 U A C C 0.428571 0.846154
62 C5P SIA 0.423729 0.893333
63 DOC 0.423529 0.890411
64 G3N 0.421569 0.890411
65 G G G C 0.421488 0.85
66 G8D 0.421053 0.907895
67 UDX 0.42 0.888889
68 UAD 0.42 0.888889
69 A G C C 0.418033 0.848101
70 2KH 0.417582 0.915493
71 3UC 0.417476 0.842105
72 4GW 0.415842 0.866667
73 UGA 0.411765 0.901408
74 V12 0.411765 0.75
75 UGB 0.411765 0.901408
76 USQ 0.411765 0.780488
77 CG2 0.410256 0.873418
78 GEO 0.407407 0.783784
79 G C C C 0.404762 0.860759
80 NVG 0.403846 0.731707
81 44P 0.402299 0.902778
82 8OD 0.402062 0.855263
83 A U C C 0.4 0.835443
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1I52; Ligand: CTP; Similar sites found: 200
This union binding pocket(no: 1) in the query (biounit: 1i52.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4F4S EFO 0.002362 0.44384 None
2 1LNX URI 0.007474 0.42199 None
3 1PTR PRB 0.03622 0.4083 None
4 4Q0A GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 0.003686 0.40457 0.847458
5 1QDS PGA 0.0007135 0.45452 1.27119
6 1JYL CDC 0.00001202 0.45377 1.27119
7 1F3L SAH 0.001563 0.40679 1.27119
8 2DTX BMA 0.0008347 0.40474 1.27119
9 1VE3 SAM 0.002179 0.409 1.32159
10 1V6A TRE 0.00422 0.43839 1.69492
11 1ME8 RVP 0.005036 0.40673 1.69492
12 3GE7 AFQ 0.0005141 0.40341 1.69492
13 1BTN I3P 0.003739 0.48462 1.88679
14 2WA4 069 0.002743 0.42576 2.11864
15 3FPZ AHZ 0.001425 0.42496 2.11864
16 3P3N AKG 0.01319 0.42125 2.11864
17 1EB9 HBA 0.0047 0.41643 2.11864
18 2BH9 NAP 0.004026 0.41074 2.11864
19 1GR0 NAD 0.003847 0.40831 2.11864
20 2OEG UPG 0.0006402 0.40615 2.11864
21 1P4C FMN 0.004146 0.40352 2.11864
22 4OYA 1VE 0.01148 0.4024 2.11864
23 1FL2 FAD 0.001111 0.40216 2.11864
24 1XIU REA 0.0002306 0.45247 2.17391
25 1C1L GAL BGC 0.01224 0.42852 2.18978
26 2PR5 FMN 0.004615 0.40107 2.27273
27 1FW1 GSH 0.001134 0.43614 2.31481
28 3S9K CIT 0.0004932 0.5618 2.54237
29 3MAG 3MA 0.0008377 0.51301 2.54237
30 4OB6 S2T 0.000755 0.43815 2.54237
31 4JWX 1N4 0.003651 0.43559 2.54237
32 1YP4 ADQ 0.0003075 0.42588 2.54237
33 2QCX PF1 0.009041 0.42345 2.54237
34 4WB7 ATP 0.003968 0.41718 2.54237
35 2CJE DUN 0.003755 0.40075 2.54237
36 3DGB MUC 0.01164 0.40068 2.54237
37 1SS4 GSH 0.0002138 0.56141 2.61438
38 1SS4 CIT 0.005116 0.49208 2.61438
39 1SAY PYR 0.01693 0.4024 2.77008
40 1SB8 UD2 0.001911 0.40543 2.84091
41 1XE7 GUN 0.001592 0.48804 2.95567
42 2ICY UPG 0.0001892 0.46904 2.9661
43 2X61 CH 0.0003806 0.41486 2.9661
44 4BJZ P3A 0.002301 0.41442 2.9661
45 4BJZ FAD 0.002301 0.41442 2.9661
46 1DLJ UGA 0.001016 0.41223 2.9661
47 1EDO NAP 0.002778 0.41047 2.9661
48 1R6D NAD 0.001944 0.40602 2.9661
49 1DLJ NAI 0.001779 0.4047 2.9661
50 4K30 NLG 0.01191 0.41313 3.125
51 1YOA FMN 0.002838 0.4946 3.14465
52 3QH2 3NM 0.0131 0.42992 3.16742
53 1V7R CIT 0.005145 0.47007 3.22581
54 4COQ SAN 0.01419 0.41976 3.23887
55 3GX0 GDS 0.001603 0.41365 3.25581
56 3F81 STT 0.01434 0.43813 3.27869
57 3ZPG 5GP 0.004557 0.4642 3.38983
58 2Q8H TF4 0.006039 0.45781 3.38983
59 2EB5 OXL 0.003363 0.44899 3.38983
60 1WDA BAG 0.001536 0.44624 3.38983
61 2Z9V PXM 0.006685 0.42411 3.38983
62 1H82 GZZ 0.0008645 0.42191 3.38983
63 1EP2 ORO 0.0001914 0.41716 3.38983
64 1H82 FAD 0.001107 0.41614 3.38983
65 2R5T ANP 0.001145 0.41492 3.38983
66 2PP3 LGT 0.005248 0.41034 3.38983
67 1DBT U5P 0.002556 0.41026 3.38983
68 1OAA OAA 0.000786 0.40986 3.38983
69 1P1M MET 0.001323 0.40918 3.38983
70 2A2X NA9 0.004192 0.40257 3.38983
71 1EP2 FAD 0.0001411 0.40059 3.38983
72 1D8C GLV 0.001918 0.48193 3.81356
73 1P7T PYR 0.003919 0.46917 3.81356
74 1RZM E4P 0.003215 0.45661 3.81356
75 3CV2 OXL 0.01407 0.4328 3.81356
76 3FC4 EDO 0.0003792 0.42825 3.81356
77 1RZM PEP 0.005948 0.42633 3.81356
78 1ZK7 FAD 0.0003711 0.42182 3.81356
79 1TFZ 869 0.00121 0.4179 3.81356
80 1U5R ATP 0.007071 0.40149 3.81356
81 1G8S MET 0.003368 0.44896 3.91304
82 3UEC ALA ARG TPO LYS 0.00374 0.45344 4.10959
83 3SHR CMP 0.001587 0.44028 4.23729
84 3K8D CTP 0.00003434 0.41823 4.23729
85 3CKJ CIT 0.002904 0.41061 4.23729
86 1H0C AOA 0.03644 0.40539 4.23729
87 2JBH 5GP 0.0001749 0.48612 4.44444
88 2F2U M77 0.003759 0.4249 4.66102
89 1Q11 TYE 0.007296 0.42245 4.66102
90 4E28 9MZ 0.01305 0.42147 4.66102
91 3T31 FAD 0.002093 0.40583 4.66102
92 3T31 DCQ 0.002346 0.40583 4.66102
93 4E28 0MZ 0.02287 0.40517 4.66102
94 3K37 BCZ 0.005889 0.40335 4.66102
95 1EJE FMN 0.004593 0.40115 4.6875
96 3F8C HT1 0.02783 0.40128 4.7619
97 1VF1 GSH 0.003443 0.40563 4.80349
98 1IIM TTP 0.00000571 0.46552 5.08475
99 3A1I UNU 0.0005109 0.46047 5.08475
100 1JV1 UD1 0.0001389 0.45236 5.08475
101 3I8P 840 0.0003851 0.44917 5.08475
102 4M5P MLA 0.01282 0.44841 5.08475
103 1H5T DAU 0.0005627 0.43562 5.08475
104 4M5P 23W 0.01475 0.43071 5.08475
105 4DYO SD4 0.003623 0.43048 5.08475
106 1CKM GTP 0.004852 0.42511 5.08475
107 4DEM YS4 0.004599 0.40913 5.08475
108 1UF5 CDT 0.01341 0.40217 5.08475
109 1ZJ6 G3D 0.004979 0.41543 5.34759
110 2PA4 UPG 0.00001557 0.48811 5.50847
111 3I0O SMI 0.004976 0.43516 5.50847
112 3I0O ADP 0.0025 0.43217 5.50847
113 4KCT PYR 0.004421 0.42682 5.50847
114 1Q3Q ANP 0.0005421 0.42426 5.50847
115 4P4T GDP 0.002348 0.41158 5.50847
116 4KCT FDP 0.006541 0.4107 5.50847
117 1ECC PCP 0.00004353 0.41001 5.50847
118 4CCO OGA 0.01697 0.40638 5.50847
119 4R33 SAH 0.0005595 0.4037 5.50847
120 4R33 TRP 0.0005595 0.4037 5.50847
121 3DJL FAD 0.007847 0.40031 5.50847
122 2Q37 3AL 0.0154 0.41297 5.52486
123 3BY8 MLT 0.001382 0.47432 5.6338
124 1UO5 PIH 0.005747 0.4771 5.88235
125 4L80 OXL 0.01868 0.41697 5.9322
126 1H7F C5P 0.0001011 0.41489 5.9322
127 4FFS BIG 0.00134 0.40555 5.9322
128 1TDF NAP 0.00497 0.40345 5.9322
129 1ULE GLA GAL NAG 0.03554 0.41134 6
130 3R4S SIA 0.02928 0.41491 6.35593
131 2XVE FAD 0.003478 0.4033 6.35593
132 1REO FAD 0.001067 0.40158 6.35593
133 4O1M NAD 0.0004225 0.40151 6.35593
134 2QLX RM4 0.01967 0.41849 6.48148
135 1Y9Q MED 0.02407 0.40897 6.77083
136 2YQS UD1 0.00005463 0.47895 6.77966
137 3LTW HLZ 0.0008495 0.47684 6.77966
138 1SQ5 PAU 0.004263 0.43265 6.77966
139 4DEC 3PG 0.00002609 0.42584 6.77966
140 4DEC UDP 0.00002609 0.42584 6.77966
141 3QDT A2G GAL 0.01641 0.42838 6.99301
142 1QD0 RR6 0.00367 0.42072 7.03125
143 3OH3 UAD 0.001411 0.4019 7.20339
144 2D7I UDP 0.006107 0.43362 7.62712
145 1F1V DHY 0.003502 0.4311 7.62712
146 4KOA NDP 0.00204 0.41772 7.62712
147 3CF6 SP1 0.002788 0.41676 7.62712
148 4FWE FAD 0.001126 0.40514 7.62712
149 1MZV AMP 0.002324 0.43348 7.65957
150 3RF4 FUN 0.002566 0.44227 7.75862
151 1KTC NGA 0.001915 0.44782 8.05085
152 1I0Z OXM 0.02675 0.42387 8.05085
153 2Y7G AAE 0.002319 0.41977 8.05085
154 1MXI SAH 0.0003643 0.44052 8.125
155 2FR6 CTN 0.0007393 0.42953 8.21918
156 2FR6 URI 0.003881 0.40377 8.21918
157 2IZ1 ATR 0.0009186 0.47526 8.47458
158 1PEA ACM 0.01665 0.42217 8.47458
159 1QO0 BMD 0.02277 0.41011 8.47458
160 1Z41 FMN 0.001212 0.4304 8.8983
161 3PLN U5P 0.006577 0.42442 8.8983
162 4RJK PYR 0.02032 0.42368 8.8983
163 1Z44 FMN 0.003399 0.41766 8.8983
164 2RGH FAD 0.0008401 0.40578 8.8983
165 1HV9 UD1 0.000001116 0.52625 9.32203
166 4KQL 1SG 0.0006719 0.43831 9.32203
167 1FWY UD1 0.00189 0.4377 9.32203
168 3JUK UPG 0.0004862 0.42291 9.32203
169 2E1A MSE 0.005111 0.42415 9.33333
170 2WGC SIA GAL BGC 0.005893 0.47648 9.35672
171 3KJQ B94 0.0008362 0.44632 9.47368
172 1TUV VK3 0.01193 0.44233 9.64912
173 2IYG FMN 0.01198 0.40018 9.67742
174 2XDQ MGX 0.00138 0.49127 9.74576
175 2C5S AMP 0.002473 0.43749 9.74576
176 4A8H PUW 0.0004551 0.40135 9.74576
177 1YRX FMN 0.004297 0.41371 9.91736
178 3KMT SAH 0.0001772 0.46736 10.084
179 1WVC CTP 0.000001026 0.55802 10.1695
180 2NVK FAD 0.0008533 0.40667 10.1695
181 2FH5 GTP 0.0007359 0.42543 10.2703
182 2V6O FAD 0.002276 0.41582 10.5932
183 1LVL FAD 0.0008029 0.40958 10.5932
184 1XX4 BAM 0.00794 0.45159 11.0169
185 3F3E LEU 0.0001575 0.42369 11.0169
186 1EYE PMM 0.00738 0.4086 11.0169
187 1Y42 TYR 0.008462 0.41963 11.4407
188 2NCD ADP 0.01897 0.40887 11.4407
189 2RDT 2RD 0.004156 0.40349 11.8644
190 1VDC FAD 0.001911 0.40196 11.8644
191 2Z49 AMG 0.02272 0.42397 12.7119
192 2YP9 SIA CMO 0.004146 0.4083 13.5593
193 4J6O CIT 0.01537 0.42621 13.9831
194 2V5E SCR 0.002284 0.4893 15
195 1W7J ADP BEF 0.00142 0.42349 15.678
196 4F8L GAL 0.03074 0.43528 17.2414
197 2Y6P CTP 0.000004455 0.43559 20.5128
198 1FRW GTP 0.0003296 0.4854 23.1959
199 4G87 UD1 0.000001253 0.52928 24.5763
200 1O9U ADZ 0.0005736 0.51116 44.4444
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