Receptor
PDB id Resolution Class Description Source Keywords
5TT5 1.55 Å EC: 6.5.1.2 ESCHERICHIA COLI LIGA (K115M) IN COMPLEX WITH NAD+ ESCHERICHIA COLI (STRAIN K12) METAL CATALYSIS COVALENT NUCLEOTIDYLTRANSFERASE LYSYL-AMP
Ref.: TWO-METAL VERSUS ONE-METAL MECHANISMS OF LYSINE ADENYLYLATION BY ATP-DEPENDENT AND NAD(+)-DEPENDENT POLYNUCLEOTIDE LIGASES. PROC. NATL. ACAD. SCI. V. 114 2592 2017 U.S.A.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:702;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
NAD A:701;
Valid;
none;
submit data
663.425 C21 H27 N7 O14 P2 c1cc(...
MG A:703;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5TT5 1.55 Å EC: 6.5.1.2 ESCHERICHIA COLI LIGA (K115M) IN COMPLEX WITH NAD+ ESCHERICHIA COLI (STRAIN K12) METAL CATALYSIS COVALENT NUCLEOTIDYLTRANSFERASE LYSYL-AMP
Ref.: TWO-METAL VERSUS ONE-METAL MECHANISMS OF LYSINE ADENYLYLATION BY ATP-DEPENDENT AND NAD(+)-DEPENDENT POLYNUCLEOTIDE LIGASES. PROC. NATL. ACAD. SCI. V. 114 2592 2017 U.S.A.
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5TT5 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5TT5 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5TT5 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAD; Similar ligands found: 220
No: Ligand ECFP6 Tc MDL keys Tc
1 A3D 0.872727 0.986111
2 NAD IBO 0.845455 0.933333
3 NHD 0.821429 0.972222
4 NAP 0.811966 0.986111
5 NAJ PYZ 0.803419 0.910256
6 NFD 0.791304 0.946667
7 NXX 0.765766 0.972603
8 DND 0.765766 0.972603
9 ZID 0.737705 0.986111
10 NAQ 0.729508 0.934211
11 NAE 0.721311 0.959459
12 NA0 0.712 0.972603
13 TAP 0.704 0.921053
14 AMP NAD 0.696 0.945946
15 NDE 0.689922 0.972603
16 NAJ 0.683333 0.972222
17 NDC 0.679389 0.934211
18 NDO 0.674603 0.958904
19 N01 0.656 0.972222
20 CNA 0.642276 0.972603
21 NBP 0.621212 0.922078
22 NAD BBN 0.609929 0.876543
23 8ID 0.609756 0.922078
24 NAD CJ3 0.601399 0.845238
25 ADP MG 0.579439 0.918919
26 A2D 0.576923 0.958333
27 ADP 0.575472 0.931507
28 NGD 0.574803 0.922078
29 BEF ADP 0.574074 0.894737
30 ADP BEF 0.574074 0.894737
31 BA3 0.566038 0.958333
32 NAD NDT 0.565789 0.755319
33 M33 0.564815 0.918919
34 ADP PO3 0.563636 0.957747
35 B4P 0.560748 0.958333
36 AP5 0.560748 0.958333
37 ATP MG 0.558559 0.918919
38 AN2 0.555556 0.918919
39 GAP 0.553571 0.932432
40 OOB 0.551724 0.972222
41 CA0 0.550459 0.932432
42 ATP 0.545455 0.931507
43 ACP 0.545455 0.906667
44 NAD TDB 0.544872 0.70297
45 ADP ALF 0.54386 0.883117
46 ALF ADP 0.54386 0.883117
47 5FA 0.540541 0.931507
48 AQP 0.540541 0.931507
49 APR 0.540541 0.931507
50 AR6 0.540541 0.931507
51 ANP MG 0.53913 0.907895
52 VO4 ADP 0.53913 0.945205
53 ADP VO4 0.53913 0.945205
54 AGS 0.535714 0.883117
55 SAP 0.535714 0.883117
56 AD9 0.535714 0.906667
57 WAQ 0.533333 0.896104
58 ABM 0.53271 0.905405
59 00A 0.529412 0.921053
60 DLL 0.529412 0.972222
61 ANP 0.526316 0.906667
62 NJP 0.526316 0.959459
63 ACQ 0.526316 0.906667
64 OAD 0.525 0.932432
65 AMP MG 0.523364 0.905405
66 ADX 0.522523 0.839506
67 5AL 0.521739 0.945205
68 A1R 0.521008 0.871795
69 9SN 0.520325 0.909091
70 AMP 0.518868 0.930556
71 A 0.518868 0.930556
72 50T 0.517857 0.893333
73 ATF 0.517241 0.894737
74 DAL AMP 0.516949 0.945205
75 3OD 0.516393 0.932432
76 1ZZ 0.516393 0.851852
77 SON 0.513514 0.92
78 PRX 0.513274 0.881579
79 SRP 0.512821 0.92
80 ADP BMA 0.512397 0.932432
81 3UK 0.512397 0.958904
82 MYR AMP 0.512195 0.851852
83 NAJ PZO 0.510949 0.909091
84 NMN 0.509434 0.875
85 AMP DBH 0.507937 0.906667
86 A22 0.504202 0.945205
87 FA5 0.504 0.945946
88 ATP A A A 0.504 0.971831
89 TYR AMP 0.5 0.945946
90 8QN 0.5 0.945205
91 NAX 0.496183 0.886076
92 PR8 0.495935 0.8625
93 PAJ 0.495868 0.873418
94 4AD 0.495868 0.933333
95 AMO 0.495868 0.92
96 ADQ 0.495868 0.932432
97 A12 0.495495 0.894737
98 AP2 0.495495 0.894737
99 ALF ADP 3PG 0.492424 0.873418
100 LA8 ALF 3PG 0.492424 0.873418
101 AHZ 0.492308 0.851852
102 YAP 0.492063 0.933333
103 FYA 0.491935 0.918919
104 AHX 0.491803 0.884615
105 4UU 0.488372 0.933333
106 5SV 0.487603 0.8375
107 TAT 0.487179 0.894737
108 APC 0.486957 0.894737
109 SRA 0.486239 0.881579
110 NAI 0.484848 0.921053
111 6V0 0.484848 0.909091
112 GTA 0.484615 0.898734
113 A A 0.483871 0.958333
114 LAD 0.483871 0.873418
115 AU1 0.482456 0.906667
116 TXE 0.481203 0.921053
117 AF3 ADP 3PG 0.481203 0.873418
118 OMR 0.481203 0.841463
119 LAQ 0.480916 0.851852
120 G3A 0.48062 0.909091
121 TXA 0.48 0.92
122 NB8 0.48 0.884615
123 ME8 0.48 0.851852
124 BIS 0.48 0.871795
125 PTJ 0.48 0.884615
126 139 0.477941 0.886076
127 LPA AMP 0.477273 0.851852
128 AR6 AR6 0.476923 0.958333
129 G5P 0.476923 0.909091
130 AFH 0.476923 0.873418
131 25L 0.47619 0.945205
132 25A 0.47541 0.958333
133 DZD 0.47482 0.897436
134 TXD 0.473684 0.921053
135 4UV 0.472868 0.933333
136 TYM 0.470149 0.945946
137 ADV 0.470085 0.894737
138 RBY 0.470085 0.894737
139 ARG AMP 0.469697 0.841463
140 4TA 0.467626 0.864198
141 48N 0.466165 0.884615
142 XAH 0.465116 0.851852
143 4UW 0.462687 0.897436
144 M24 0.461538 0.886076
145 IOT 0.459854 0.821429
146 T5A 0.456522 0.853659
147 EAD 0.455782 0.886076
148 MAP 0.455285 0.883117
149 BT5 0.453901 0.821429
150 A4P 0.452555 0.833333
151 UP5 0.451852 0.933333
152 PAP 0.445378 0.917808
153 AP0 0.445255 0.884615
154 4TC 0.445255 0.909091
155 YLP 0.444444 0.831325
156 P1H 0.443709 0.864198
157 AOC 0.442478 0.810811
158 Z5A 0.439189 0.833333
159 2A5 0.436975 0.857143
160 G A A A 0.43662 0.909091
161 COD 0.43662 0.802326
162 ADJ 0.435714 0.841463
163 YLC 0.434783 0.851852
164 YLB 0.434783 0.831325
165 U A G G 0.433566 0.921053
166 ATR 0.433333 0.90411
167 7MD 0.432836 0.851852
168 G5A 0.429752 0.790698
169 PO4 PO4 A A A A PO4 0.429688 0.943662
170 TAD 0.42963 0.873418
171 5AS 0.42735 0.770115
172 BTX 0.426573 0.831325
173 YLA 0.425532 0.831325
174 DSZ 0.425197 0.790698
175 NCN 0.424779 0.805556
176 UPA 0.42446 0.921053
177 VMS 0.424 0.8
178 54H 0.424 0.8
179 N0B 0.422819 0.853659
180 6AD 0.422764 0.85
181 AYB 0.422535 0.821429
182 7D3 0.422414 0.844156
183 YLY 0.421769 0.821429
184 TSB 0.420635 0.809524
185 ODP 0.41958 0.922078
186 AV2 0.419355 0.855263
187 FB0 0.419355 0.775281
188 A5A 0.419355 0.819277
189 NNR 0.419048 0.739726
190 A A A 0.418605 0.918919
191 LEU LMS 0.418605 0.793103
192 649 0.417266 0.775281
193 NMN AMP PO4 0.416667 0.933333
194 SSA 0.416 0.790698
195 P5A 0.415385 0.755556
196 LSS 0.414062 0.772727
197 A2R 0.412698 0.918919
198 52H 0.412698 0.790698
199 JB6 0.412214 0.896104
200 5N5 0.411215 0.783784
201 YSA 0.410448 0.811765
202 5CA 0.409449 0.790698
203 53H 0.409449 0.790698
204 ITT 0.408333 0.878378
205 7D4 0.408333 0.844156
206 NA7 0.407692 0.894737
207 5CD 0.407407 0.794521
208 0WD 0.406897 0.909091
209 A3P 0.40678 0.930556
210 AVV 0.40625 0.860759
211 RAB 0.40566 0.808219
212 ADN 0.40566 0.808219
213 XYA 0.40566 0.808219
214 FDA 0.405063 0.823529
215 GSU 0.40458 0.790698
216 7MC 0.404255 0.831325
217 NSS 0.403101 0.811765
218 6FA 0.402516 0.853659
219 NVA LMS 0.4 0.793103
220 PPS 0.4 0.817073
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5TT5; Ligand: NAD; Similar sites found: 54
This union binding pocket(no: 1) in the query (biounit: 5tt5.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2PZI AXX 0.008508 0.41954 0.734214
2 4IDT T28 0.01213 0.40473 1.40449
3 3FW3 GLC 0.007894 0.47007 1.8797
4 4YMJ 4EJ 0.0007425 0.49149 1.97368
5 4XH0 ADP 0.001046 0.48227 1.98511
6 5AWM ANP 0.001878 0.45622 2.28426
7 3X01 AMP 0.009695 0.43135 2.29008
8 3WVR AMP 0.007876 0.41718 2.46085
9 4DFU QUE 0.004097 0.44949 2.48447
10 2QLU ADE 0.03088 0.40212 2.54777
11 3F10 8HG 0.01105 0.40318 2.60492
12 1VRP IOM 0.02292 0.40996 2.62467
13 3PLS ANP 0.008731 0.41135 2.68456
14 1BYG STU 0.003974 0.43123 2.8777
15 3HZT J60 0.004284 0.43849 2.99786
16 2ZV2 609 0.003192 0.44481 3.02013
17 4WOV 3SM 0.003329 0.43925 3.15457
18 4AU8 Z3R 0.009556 0.42122 3.18379
19 1JPA ANP 0.000776 0.45927 3.20513
20 4CFU 2WC 0.002846 0.43807 3.30033
21 4BCM T7Z 0.0008641 0.48466 3.32226
22 4BCN T9N 0.002644 0.44408 3.33333
23 5DA3 58V 0.00804 0.42494 3.39623
24 4WNP 3RJ 0.004751 0.43179 3.83275
25 3TY5 ADP 0.00002725 0.44505 3.87409
26 2A19 ANP 0.001955 0.45535 4
27 3GGF GVD 0.009679 0.41295 4.31894
28 1XDN ATP 0.0000006011 0.6113 4.33213
29 1V0O INR 0.01153 0.40235 4.51389
30 2IF8 ADP 0.02939 0.40472 4.6832
31 1UNH IXM 0.002176 0.44816 4.80769
32 1S68 AMP 0.0000001833 0.46229 4.81928
33 4Y8D 49J 0.004623 0.44675 5
34 4AUA 4AU 0.0028 0.43417 5.21173
35 3VSV XYS 0.02433 0.41402 5.64263
36 2CFM AMP 0.00002895 0.54575 5.88235
37 4X7Q 3YR 0.01418 0.40509 6.08974
38 5TT6 ATP 0.00002202 0.50841 6.59898
39 4EAX S12 0.0242 0.41071 6.66667
40 1K3A ACP 0.005483 0.42878 6.68896
41 4D2S DYK 0.007198 0.42306 6.69014
42 2Q4X HMH 0.0395 0.40227 6.78733
43 5COU ATP 0.000001632 0.48906 7.05882
44 5C1P ADP 0.002974 0.44161 7.51634
45 3HMO STU 0.004916 0.42288 7.60234
46 5HVJ ANP 0.001439 0.47448 7.93651
47 5LPB ADP 0.003478 0.44297 8.78378
48 1CKM GTP 0.00006754 0.49265 9.39394
49 2QX0 PH2 0.03139 0.40574 9.43396
50 3B6R CRN 0.006253 0.43416 10.4987
51 4CQK PIO 0.03276 0.40152 10.6383
52 3HAV ATP 0.002324 0.46667 11.7057
53 3H9R TAK 0.02023 0.40899 13.7615
54 2F57 23D 0.002943 0.43738 18.9274
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