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Receptor
PDB id Resolution Class Description Source Keywords
1OWB 2.2 Å EC: 2.3.3.1 THREE DIMENSIONAL STRUCTURE ANALYSIS OF THE VARIANT R109L NA OF TYPE II CITRATE SYNTHASE FROM E. COLI ESCHERICHIA COLI ALLOSTERY NADH TYPE II CITRATE SYNTHASE E. COLI R109L TRANSFERASE
Ref.: PROBING THE ROLES OF KEY RESIDUES IN THE UNIQUE REG NADH BINDING SITE OF TYPE II CITRATE SYNTHASE OF ESCHERICHIA COLI. J.BIOL.CHEM. V. 278 35435 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAD A:3000;
B:3001;
Valid;
Valid;
none;
none;
Kd = 1.16 uM
663.425 C21 H27 N7 O14 P2 c1cc(...
SO4 A:2002;
A:2004;
A:2005;
A:2006;
B:2001;
B:2003;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1OWB 2.2 Å EC: 2.3.3.1 THREE DIMENSIONAL STRUCTURE ANALYSIS OF THE VARIANT R109L NA OF TYPE II CITRATE SYNTHASE FROM E. COLI ESCHERICHIA COLI ALLOSTERY NADH TYPE II CITRATE SYNTHASE E. COLI R109L TRANSFERASE
Ref.: PROBING THE ROLES OF KEY RESIDUES IN THE UNIQUE REG NADH BINDING SITE OF TYPE II CITRATE SYNTHASE OF ESCHERICHIA COLI. J.BIOL.CHEM. V. 278 35435 2003
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1OWB Kd = 1.16 uM NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 1NXG - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
3 4JAF - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
4 4JAG - OAA C4 H3 O5 C(C(=O)C(=....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1OWB Kd = 1.16 uM NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 1NXG - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
3 4JAF - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
4 4JAG - OAA C4 H3 O5 C(C(=O)C(=....
5 2H12 Kd = 21.1 uM OAA C4 H3 O5 C(C(=O)C(=....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1OWB Kd = 1.16 uM NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 1NXG - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
3 4JAF - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
4 4JAG - OAA C4 H3 O5 C(C(=O)C(=....
5 2H12 Kd = 21.1 uM OAA C4 H3 O5 C(C(=O)C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAD; Similar ligands found: 230
No: Ligand ECFP6 Tc MDL keys Tc
1 A3D 0.872727 0.986111
2 NHD 0.821429 0.972222
3 NAP 0.811966 0.986111
4 NFD 0.791304 0.946667
5 NXX 0.765766 0.972603
6 DND 0.765766 0.972603
7 AMP NAD 0.74359 0.972222
8 ZID 0.737705 0.986111
9 NAQ 0.729508 0.934211
10 NAE 0.721311 0.959459
11 NA0 0.712 0.972603
12 TAP 0.704 0.921053
13 NDE 0.689922 0.972603
14 NAJ 0.683333 0.972222
15 NDC 0.679389 0.934211
16 NDO 0.674603 0.958904
17 N01 0.656 0.972222
18 CNA 0.642276 0.972603
19 NBP 0.621212 0.922078
20 8ID 0.609756 0.922078
21 A2D 0.576923 0.958333
22 ADP 0.575472 0.931507
23 NGD 0.574803 0.922078
24 BA3 0.566038 0.958333
25 M33 0.564815 0.918919
26 ADP PO3 0.563636 0.957747
27 B4P 0.560748 0.958333
28 AP5 0.560748 0.958333
29 AN2 0.555556 0.918919
30 AT4 0.555556 0.894737
31 GAP 0.553571 0.932432
32 OOB 0.551724 0.972222
33 CA0 0.550459 0.932432
34 9JJ 0.546053 0.898734
35 HEJ 0.545455 0.931507
36 ACP 0.545455 0.906667
37 ATP 0.545455 0.931507
38 DQV 0.544 0.972222
39 ADP ALF 0.54386 0.883117
40 ALF ADP 0.54386 0.883117
41 DAL AMP 0.543103 0.945205
42 APR 0.540541 0.931507
43 AQP 0.540541 0.931507
44 AR6 0.540541 0.931507
45 5FA 0.540541 0.931507
46 ADP VO4 0.53913 0.945205
47 VO4 ADP 0.53913 0.945205
48 AD9 0.535714 0.906667
49 SAP 0.535714 0.883117
50 AGS 0.535714 0.883117
51 WAQ 0.533333 0.896104
52 ABM 0.53271 0.905405
53 DLL 0.529412 0.972222
54 00A 0.529412 0.921053
55 ACQ 0.526316 0.906667
56 NJP 0.526316 0.959459
57 ANP 0.526316 0.906667
58 OAD 0.525 0.932432
59 ADX 0.522523 0.839506
60 5AL 0.521739 0.945205
61 A1R 0.521008 0.871795
62 9SN 0.520325 0.909091
63 A 0.518868 0.930556
64 AMP 0.518868 0.930556
65 50T 0.517857 0.893333
66 ATF 0.517241 0.894737
67 1ZZ 0.516393 0.851852
68 3OD 0.516393 0.932432
69 SON 0.513514 0.92
70 PRX 0.513274 0.881579
71 6YZ 0.512821 0.906667
72 SRP 0.512821 0.92
73 9X8 0.512397 0.883117
74 ADP BMA 0.512397 0.932432
75 3UK 0.512397 0.958904
76 MYR AMP 0.512195 0.851852
77 NAJ PZO 0.510949 0.909091
78 NMN 0.509434 0.875
79 A3R 0.508333 0.871795
80 B5V 0.508197 0.945946
81 AMP DBH 0.507937 0.906667
82 A22 0.504202 0.945205
83 ATP A A A 0.504 0.971831
84 B5M 0.504 0.933333
85 FA5 0.504 0.945946
86 8QN 0.5 0.945205
87 NAX 0.496183 0.886076
88 TYR AMP 0.496063 0.933333
89 PR8 0.495935 0.8625
90 AMO 0.495868 0.92
91 ADQ 0.495868 0.932432
92 4AD 0.495868 0.933333
93 PAJ 0.495868 0.873418
94 A12 0.495495 0.894737
95 AP2 0.495495 0.894737
96 AHZ 0.492308 0.851852
97 YAP 0.492063 0.933333
98 FYA 0.491935 0.918919
99 AHX 0.491803 0.884615
100 4UU 0.488372 0.933333
101 5SV 0.487603 0.8375
102 TAT 0.487179 0.894737
103 T99 0.487179 0.894737
104 APC 0.486957 0.894737
105 SRA 0.486239 0.881579
106 6V0 0.484848 0.909091
107 NAI 0.484848 0.921053
108 GTA 0.484615 0.898734
109 A A 0.483871 0.958333
110 LAD 0.483871 0.873418
111 AU1 0.482456 0.906667
112 F2R 0.481752 0.831325
113 OMR 0.481203 0.841463
114 TXE 0.481203 0.921053
115 AF3 ADP 3PG 0.481203 0.873418
116 LAQ 0.480916 0.851852
117 G3A 0.48062 0.909091
118 B5Y 0.480315 0.933333
119 NB8 0.48 0.884615
120 TXA 0.48 0.92
121 BIS 0.48 0.871795
122 ME8 0.48 0.851852
123 PTJ 0.48 0.884615
124 139 0.477941 0.886076
125 LPA AMP 0.477273 0.851852
126 AFH 0.476923 0.873418
127 AR6 AR6 0.476923 0.958333
128 G5P 0.476923 0.909091
129 ARG AMP 0.476923 0.841463
130 25L 0.47619 0.945205
131 NAJ PYZ 0.475524 0.864198
132 25A 0.47541 0.958333
133 9ZA 0.47541 0.896104
134 9ZD 0.47541 0.896104
135 DZD 0.47482 0.897436
136 TXD 0.473684 0.921053
137 4UV 0.472868 0.933333
138 TYM 0.470149 0.945946
139 RBY 0.470085 0.894737
140 ADV 0.470085 0.894737
141 4TA 0.467626 0.864198
142 48N 0.466165 0.884615
143 XAH 0.465116 0.851852
144 4UW 0.462687 0.897436
145 M24 0.461538 0.886076
146 80F 0.460993 0.853659
147 IOT 0.459854 0.821429
148 T5A 0.456522 0.853659
149 EAD 0.455782 0.886076
150 MAP 0.455285 0.883117
151 GA7 0.454545 0.894737
152 BT5 0.453901 0.821429
153 A4P 0.452555 0.833333
154 UP5 0.451852 0.933333
155 PAP 0.445378 0.917808
156 4TC 0.445255 0.909091
157 AP0 0.445255 0.884615
158 YLP 0.444444 0.831325
159 P1H 0.443709 0.864198
160 AOC 0.442478 0.810811
161 Z5A 0.439189 0.833333
162 LMS 0.4375 0.817073
163 2A5 0.436975 0.857143
164 A G 0.43662 0.921053
165 G A A A 0.43662 0.909091
166 COD 0.43662 0.802326
167 ADJ 0.435714 0.841463
168 YLB 0.434783 0.831325
169 YLC 0.434783 0.851852
170 U A G G 0.433566 0.921053
171 ATR 0.433333 0.90411
172 7MD 0.432836 0.851852
173 8X1 0.432 0.764045
174 G5A 0.429752 0.790698
175 PO4 PO4 A A A A PO4 0.429688 0.943662
176 TAD 0.42963 0.873418
177 5AS 0.42735 0.770115
178 BTX 0.426573 0.831325
179 YLA 0.425532 0.831325
180 DSZ 0.425197 0.790698
181 NCN 0.424779 0.805556
182 UPA 0.42446 0.921053
183 8PZ 0.424242 0.811765
184 VMS 0.424 0.8
185 54H 0.424 0.8
186 9K8 0.423077 0.744444
187 N0B 0.422819 0.853659
188 6AD 0.422764 0.85
189 AYB 0.422535 0.821429
190 7D3 0.422414 0.844156
191 YLY 0.421769 0.821429
192 TSB 0.420635 0.809524
193 ODP 0.41958 0.922078
194 AV2 0.419355 0.855263
195 FB0 0.419355 0.775281
196 A5A 0.419355 0.819277
197 NNR 0.419048 0.739726
198 A A A 0.418605 0.918919
199 U A 0.417808 0.946667
200 649 0.417266 0.775281
201 NMN AMP PO4 0.416667 0.933333
202 SSA 0.416 0.790698
203 P5A 0.415385 0.755556
204 LSS 0.414062 0.772727
205 A2R 0.412698 0.918919
206 52H 0.412698 0.790698
207 JB6 0.412214 0.896104
208 5N5 0.411215 0.783784
209 YSA 0.410448 0.811765
210 53H 0.409449 0.790698
211 5CA 0.409449 0.790698
212 ITT 0.408333 0.878378
213 7D4 0.408333 0.844156
214 NA7 0.407692 0.894737
215 LEU LMS 0.407692 0.784091
216 5CD 0.407407 0.794521
217 0WD 0.406897 0.909091
218 A3P 0.40678 0.930556
219 HFD 0.406504 0.883117
220 AVV 0.40625 0.860759
221 RAB 0.40566 0.808219
222 XYA 0.40566 0.808219
223 ADN 0.40566 0.808219
224 FDA 0.405063 0.823529
225 GSU 0.40458 0.790698
226 7MC 0.404255 0.831325
227 NSS 0.403101 0.811765
228 6FA 0.402516 0.853659
229 PPS 0.4 0.817073
230 NVA LMS 0.4 0.784091
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1OWB; Ligand: NAD; Similar sites found with APoc: 10
This union binding pocket(no: 1) in the query (biounit: 1owb.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4U8P UDP 3.0445
2 2V5E SCR 3.5
3 5N6N SUC 3.75
4 4LIK CIT 4.08163
5 3KP6 SAL 4.63576
6 1A5Z FBP 4.70219
7 5WJ6 B4A 5.15223
8 1XPJ TLA 6.34921
9 6C0B MLI 12.1795
10 4F4S EFO 13.1579
Pocket No.: 2; Query (leader) PDB : 1OWB; Ligand: NAD; 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: 1owb.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1OWB; Ligand: NAD; 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: 1owb.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1OWB; Ligand: NAD; Similar sites found with APoc: 39
This union binding pocket(no: 4) in the query (biounit: 1owb.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 2EA1 GPG None
3 3O01 DXC 1.2987
4 3B9Z CO2 1.80412
5 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 2.38095
6 1GEG GLC 3.125
7 2GBB CIT 3.20513
8 3UNN MET GLU ASP TPO GLN ALA ILE ASP 3.53982
9 3E70 GDP 3.65854
10 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 3.91304
11 3CV2 COA 4.21546
12 5LX9 OLB 4.23453
13 2VWA PTY 4.9505
14 5OCA 9QZ 5.06912
15 1R6N 434 5.21327
16 6BR9 PGV 5.29248
17 5V4R MGT 5.55556
18 5W7B MYR 5.67376
19 5IJJ I6P 5.72917
20 5HCN DAO 5.74713
21 5C1M OLC 6.4
22 4WGF HX2 6.82927
23 4UCC ZKW 6.86695
24 5A9A UTP 6.99588
25 4V3I ASP LEU THR ARG PRO 7.25995
26 6BR8 PGV 7.53968
27 2GWH PCI 7.71812
28 5UGW GSH 8.57143
29 5N26 CPT 9.34066
30 5AZC PGT 11.6667
31 2Y69 CHD 13.4021
32 3RV5 DXC 13.4831
33 2BHW NEX 14.2241
34 5Z84 CHD 16.3265
35 5W97 CHD 16.3265
36 5ZCO CHD 16.3265
37 4RJD TFP 21.2121
38 5NNT DPV 24.3243
39 2D5X L35 26.2411
Pocket No.: 5; Query (leader) PDB : 1OWB; Ligand: NAD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 1owb.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1OWB; Ligand: NAD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 1owb.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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