Receptor
PDB id Resolution Class Description Source Keywords
1T90 2.5 Å EC: 1.2.1.27 CRYSTAL STRUCTURE OF METHYLMALONATE SEMIALDEHYDE DEHYDROGENASE FROM BACILLUS SUBTILIS BACILLUS SUBTILIS OXIDOREDUCTASE NAD
Ref.: CRYSTAL STRUCTURE ANALYSIS OF METHYLMALONATE-SEMIALDEHYDE DEHYDROGENASE FROM BACILLUS SUBTILIS. TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAD A:1490;
B:2490;
C:3490;
D:4490;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
663.425 C21 H27 N7 O14 P2 c1cc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1T90 2.5 Å EC: 1.2.1.27 CRYSTAL STRUCTURE OF METHYLMALONATE SEMIALDEHYDE DEHYDROGENASE FROM BACILLUS SUBTILIS BACILLUS SUBTILIS OXIDOREDUCTASE NAD
Ref.: CRYSTAL STRUCTURE ANALYSIS OF METHYLMALONATE-SEMIALDEHYDE DEHYDROGENASE FROM BACILLUS SUBTILIS. TO BE PUBLISHED
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1T90 - 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 1 families.
1 1T90 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
50% Homology Family (52)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5AC1 - TXE C21 H31 N7 O14 P2 c1nc(c2c(n....
2 5L2O ic50 = 0.76 uM 6ZW C14 H17 N O2 CCN(CC)c1c....
3 5L2N ic50 = 2.8 uM 6ZU C18 H16 O5 S CC1=C(C(=O....
4 1BXS - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
5 5ABM - TXE C21 H31 N7 O14 P2 c1nc(c2c(n....
6 5L2M Ki = 170 nM 6ZY C22 H25 N O4 Cc1c(oc2c1....
7 4X4L ic50 = 4.6 uM 3XG C21 H25 N3 O3 S2 CCOC(=O)CS....
8 5AC0 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
9 4WP7 ic50 = 0.8 uM 3SR C22 H30 N6 O4 CC(C)CCn1c....
10 4WB9 - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
11 4WPN ic50 = 0.21 uM 3ST C19 H30 N6 O3 CC(C)CCn1c....
12 5AC2 - TXE C21 H31 N7 O14 P2 c1nc(c2c(n....
13 4I9B - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
14 5N5S Kd = 31 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
15 4PZ2 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
16 1WNB - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
17 3IWK - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
18 4A0M - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
19 4GNZ - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
20 3RHR Kd = 5.7 uM NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
21 3RHJ Kd = 0.0073 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
22 4GO2 - TAP C21 H28 N7 O16 P3 S c1cc(c[n+]....
23 2O2R - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
24 3RHL - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
25 3RHO Kd = 0.26 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
26 3RHQ Kd = 9.2 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
27 2O2Q - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
28 3JZ4 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
29 1O01 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
30 2ONM - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
31 2VLE - DZN C21 H20 O9 c1cc(ccc1C....
32 3INL - BXB C15 H11 Cl2 N O3 c1cc(c(c(c....
33 3SZ9 - I3E C11 H14 O CCc1ccc(cc....
34 4FR8 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
35 1O04 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
36 3INJ - BXB C15 H11 Cl2 N O3 c1cc(c(c(c....
37 2ONP - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
38 1O02 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
39 5L13 Ki = 19 nM 6ZE C17 H18 O3 CCCC1=C(c2....
40 1NZX - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
41 4KWG ic50 = 2.4 uM 2AK C9 H6 Br N O2 Cc1cc2c(c(....
42 4KWF ic50 = 82 uM 3AK C15 H11 N O2 c1ccc(cc1)....
43 4FQF - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
44 1NZZ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
45 5X5U - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
46 2W8Q - SIN C4 H6 O4 O=C([O-])C....
47 2W8R - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
48 2IMP - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
49 3ZQA - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
50 1O9J - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
51 4I8P - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
52 1T90 - 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 : 1T90; Ligand: NAD; 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: 1t90.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1T90; Ligand: NAD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1t90.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1T90; Ligand: NAD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1t90.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1T90; Ligand: NAD; Similar sites found: 114
This union binding pocket(no: 4) in the query (biounit: 1t90.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1U4L H1S 0.0111 0.44576 None
2 1OFL NGK GCD 0.01824 0.41718 1.4553
3 1KAE NAD 0.01634 0.41367 1.6129
4 2J44 GLC GLC GLC 0.01252 0.42024 1.84332
5 2Z4T C5P 0.01581 0.41826 1.85185
6 1SES AMP 0.02651 0.41061 1.90024
7 5TSH ANP 0.02803 0.40553 2.05761
8 1V59 NAD 0.02076 0.40849 2.09205
9 3W6X HZP 0.008508 0.44055 2.18341
10 1KYZ SAH 0.01109 0.41119 2.46575
11 1YAA MAE 0.04828 0.40165 2.6699
12 2IBN I1N 0.02678 0.41037 2.8
13 1QPR PHT 0.03483 0.4125 2.8169
14 5L2R MLA 0.03444 0.4124 2.88066
15 2D2I NAP 0.008114 0.40202 2.89474
16 5MX4 HPA 0.03422 0.40569 3.00429
17 3QPB R1P 0.03522 0.40043 3.19149
18 1TZD ADP 0.04736 0.40323 3.27273
19 5KJW 53C 0.03313 0.41082 3.27869
20 4B4Q A2G GAL NAG FUC GAL GLC 0.02608 0.41508 3.31126
21 1YFS ALA 0.02261 0.42163 3.44086
22 3DXY SAM 0.005541 0.437 3.66972
23 1VKF CIT 0.02693 0.41415 3.7234
24 4XFR CIT 0.0262 0.41785 3.74707
25 5DYO FLU 0.03726 0.40585 3.77358
26 4Z7X 3CX 0.02273 0.42263 3.78151
27 5IFK HPA 0.007119 0.44956 3.84615
28 5DNC ASN 0.03788 0.40244 3.90947
29 2WDA L42 0.04892 0.4011 3.90947
30 2NU8 COA 0.00326 0.40995 4.16667
31 1V6A TRE 0.04618 0.40297 4.21687
32 3EFS BTN 0.01301 0.40477 4.29185
33 1WDK NAD 0.008086 0.40208 4.32099
34 4Z1D PEP 0.04946 0.40041 4.34783
35 2IMG MLT 0.01708 0.41982 4.63576
36 1VMK GUN 0.007342 0.44922 4.69314
37 2B7N NTM 0.02588 0.41753 4.7619
38 3QSB 743 0.01248 0.42349 5.19126
39 1X8X TYR 0.03541 0.40031 5.2795
40 2C5S AMP 0.01421 0.42479 5.32688
41 4MJ0 SIA SIA 0.02126 0.42102 5.45455
42 3TY3 GGG 0.02955 0.4115 5.46448
43 2YY8 MTA 0.0213 0.40793 5.47264
44 5E5U MLI 0.01347 0.44092 5.52764
45 1Z34 2FD 0.02613 0.40349 5.53191
46 2ZWI C5P 0.01329 0.4221 5.63003
47 5BXV MGP 0.0459 0.4058 5.72917
48 1EJH M7G 0.04782 0.40653 5.78947
49 4RYV ZEA 0.03202 0.40256 5.80645
50 3RK0 AMP 0.02476 0.40466 5.90717
51 1RYD GLC 0.04035 0.40618 5.94315
52 3QV1 NAD 0.005766 0.40008 6.09756
53 1KYQ NAD 0.01209 0.40944 6.20438
54 5CDH TLA 0.01043 0.43399 6.25
55 3PA8 621 0.02836 0.41312 6.29921
56 2YN4 39J 0.02288 0.41999 6.35593
57 3LGS SAH 0.02394 0.40539 6.36704
58 3PNA CMP 0.03504 0.40423 6.49351
59 4JGT PYR 0.03515 0.4051 6.68896
60 4WCX MET 0.0002279 0.53397 6.875
61 3UDG TMP 0.04901 0.4046 6.97674
62 5L8N 6RQ 0.02786 0.41453 7.03125
63 4V3C C 0.00657 0.42542 7.47423
64 2JE7 XMM 0.0291 0.41252 7.53138
65 4CIB 7UZ 0.02987 0.41325 7.91209
66 3H0L ADP 0.03342 0.40161 8.51064
67 2IU8 PLM 0.001796 0.43641 8.55615
68 5FYR INS 0.01556 0.42791 8.72483
69 2JK0 ASP 0.02738 0.41527 8.92308
70 1L5Y BEF 0.01985 0.42323 9.03226
71 1HXD BTN 0.008466 0.41007 9.34579
72 5NCF 8T5 0.03292 0.40963 9.73451
73 3BJE URA 0.02557 0.41399 10.0287
74 1BW9 PPY 0.02503 0.401 10.3933
75 1C1X HFA 0.01879 0.41065 10.4225
76 2XG5 EC5 0.0002466 0.5384 10.5505
77 2XG5 EC2 0.0002466 0.5384 10.5505
78 5A7C 5D4 0.04867 0.40006 10.6195
79 1ZQ9 SAM 0.002662 0.43612 10.8772
80 2HIM ASP 0.006678 0.44983 11.1732
81 1IK4 PGH 0.01559 0.41468 11.1842
82 5FUI APY 0.00245 0.44762 11.3636
83 4YJK URA 0.03383 0.40348 11.9048
84 3DZ6 M8E 0.004108 0.42757 11.9403
85 1I7M CG 0.01377 0.4255 11.9403
86 1UYY BGC BGC 0.01023 0.43689 12.2137
87 4G86 BNT 0.01073 0.43418 12.3239
88 2FKA BEF 0.03038 0.41938 12.4031
89 1J2Z SOG 0.02813 0.40925 12.5926
90 1JG3 ADN 0.01612 0.40052 15.7447
91 3W9F I3P 0.04531 0.40504 16.1538
92 3IWD M2T 0.02795 0.41347 16.1765
93 5C79 PBU 0.02523 0.41862 18
94 2Y69 CHD 0.03703 0.40953 24.3243
95 5TVF CGQ 0.01668 0.41322 25.8824
96 5T46 MGP 0.03463 0.41256 28.7879
97 4NS3 NAD 0.00000009124 0.63859 30.0412
98 5JFL NAD 0.00000003537 0.59549 31.1069
99 1EZ0 NAP 0.00000006943 0.57343 32.5103
100 4LH0 GLV 0.00000000009568 0.69222 32.716
101 2Y5D NAP 0.000000004458 0.63653 35.1852
102 3HAZ NAD 0.000000000009984 0.72401 37.2428
103 4OE4 NAD 0.000000001056 0.72638 41.5638
104 3SZB I1E 0.03365 0.40928 42.0043
105 4YWV SSN 0.00000001478 0.59842 42.3656
106 5KF6 NAD 0.0000000000005049 0.75115 43.0041
107 3VZ3 NAP 0.00000000007803 0.68312 43.5449
108 3VZ3 SSN 0.0000000002343 0.62604 43.5449
109 4I3V NAD 0.000000000007968 0.71997 44.0329
110 4ZUL UN1 0.00000000106 0.64741 44.0329
111 1KY8 NAP 0.000000000004389 0.62935 44.0329
112 5UCD NAP 0.000000000001903 0.77724 44.639
113 3EFV NAD 0.0000000002765 0.67649 45.2381
114 3IWJ NAD 0.000000008817 0.69361 49.3827
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