Receptor
PDB id Resolution Class Description Source Keywords
2NSY 2 Å EC: 6.3.5.1 CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACI SUBTILIS IN COMPLEX WITH NAD-ADENYLATE BACILLUS SUBTILIS LIGASE AMIDOTRANSFERASE NH3 DEPENDENT ATP PYROPHOSPHATASE
Ref.: A NOVEL DEAMIDO-NAD+-BINDING SITE REVEALED BY THE T NAD-ADENYLATE INTERMEDIATE IN THE NAD+ SYNTHETASE S STRUCTURE V. 6 1129 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AMP NAD A:300;
B:302;
Valid;
Valid;
none;
none;
submit data
991.607 n/a P(=O)...
GOL A:308;
B:309;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MG A:304;
A:305;
B:306;
B:307;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
POP A:863;
B:862;
Invalid;
Invalid;
none;
none;
submit data
175.959 H2 O7 P2 O[P@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1KQP 1.03 Å EC: 6.3.5.1 NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A BACILLUS SUBTILIS LIGASE AMIDOTRANSFERASE ATP PYROPHOSPHATASE NAD-ADENYLATE
Ref.: NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILI RESOLUTION. ACTA CRYSTALLOGR.,SECT.D V. 58 1138 2002
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1EE1 - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
2 1IH8 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
3 2NSY - AMP NAD n/a n/a
4 1NSY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 1IFX - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
6 1FYD - AMP C10 H14 N5 O7 P c1nc(c2c(n....
7 1KQP - ADJ C31 H44 N11 O21 P3 c1nc(c2c(n....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1EE1 - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
2 1IH8 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
3 2NSY - AMP NAD n/a n/a
4 1NSY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 1IFX - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
6 1FYD - AMP C10 H14 N5 O7 P c1nc(c2c(n....
7 1KQP - ADJ C31 H44 N11 O21 P3 c1nc(c2c(n....
8 2PZA - AMP C10 H14 N5 O7 P c1nc(c2c(n....
9 2PZ8 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1EE1 - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
2 1IH8 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
3 2NSY - AMP NAD n/a n/a
4 1NSY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 1IFX - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
6 1FYD - AMP C10 H14 N5 O7 P c1nc(c2c(n....
7 1KQP - ADJ C31 H44 N11 O21 P3 c1nc(c2c(n....
8 1WXI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
9 1WXG - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
10 1WXH - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
11 1WXE - AMP C10 H14 N5 O7 P c1nc(c2c(n....
12 2PZA - AMP C10 H14 N5 O7 P c1nc(c2c(n....
13 2PZ8 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AMP NAD; Similar ligands found: 205
No: Ligand ECFP6 Tc MDL keys Tc
1 AMP NAD 1 1
2 A3D 0.745763 0.958904
3 NAD 0.74359 0.972222
4 N01 0.696721 0.972222
5 NXX 0.689655 0.972603
6 DND 0.689655 0.972603
7 NAJ 0.642276 0.972222
8 NA0 0.609023 0.945946
9 NHD 0.606299 0.945205
10 NAP 0.606061 0.958904
11 ZID 0.606061 0.958904
12 NAQ 0.598485 0.909091
13 GAP 0.59633 0.958904
14 ADP PO3 0.592593 0.957747
15 NAE 0.590909 0.933333
16 TAP 0.589552 0.896104
17 NFD 0.584615 0.921053
18 NDC 0.582734 0.909091
19 ALF ADP 0.571429 0.883117
20 ADP ALF 0.571429 0.883117
21 NDE 0.568345 0.945946
22 ADP VO4 0.566372 0.918919
23 VO4 ADP 0.566372 0.918919
24 DAL AMP 0.556522 0.972222
25 OOB 0.538462 0.972222
26 ADP BMA 0.537815 0.958904
27 MYR AMP 0.53719 0.875
28 TYR AMP 0.532258 0.959459
29 CNA 0.530303 0.945946
30 ATP A A A 0.528455 0.971831
31 AHZ 0.527559 0.875
32 NAJ PZO 0.522059 0.909091
33 ARG AMP 0.511811 0.864198
34 AR6 AR6 0.511811 0.985915
35 LPA AMP 0.511628 0.875
36 CA0 0.508929 0.932432
37 A 0.504673 0.90411
38 AMP 0.504673 0.90411
39 A2D 0.504587 0.931507
40 ABM 0.504587 0.88
41 ADP 0.504505 0.905405
42 00A 0.504132 0.921053
43 AF3 ADP 3PG 0.503817 0.897436
44 AN2 0.5 0.893333
45 APC 0.5 0.87013
46 NDO 0.496454 0.932432
47 9SN 0.496 0.909091
48 A12 0.495495 0.87013
49 AP2 0.495495 0.87013
50 BA3 0.495495 0.931507
51 B5M 0.492063 0.933333
52 DLL 0.491803 0.972222
53 ACP 0.491228 0.881579
54 AP5 0.491071 0.931507
55 B4P 0.491071 0.931507
56 3UK 0.487805 0.958904
57 SON 0.486726 0.92
58 AT4 0.486726 0.87013
59 NAJ PYZ 0.485915 0.864198
60 AMP DBH 0.484375 0.932432
61 B5V 0.483871 0.945946
62 WAQ 0.483871 0.896104
63 A A 0.483871 0.931507
64 5AL 0.483051 0.945205
65 M33 0.482456 0.893333
66 FA5 0.480315 0.945946
67 4TA 0.478261 0.864198
68 HEJ 0.478261 0.905405
69 ATP 0.478261 0.905405
70 SRP 0.475 0.92
71 ACQ 0.474576 0.881579
72 5FA 0.474138 0.905405
73 AR6 0.474138 0.931507
74 APR 0.474138 0.931507
75 AQP 0.474138 0.905405
76 SRA 0.472727 0.857143
77 4AD 0.471545 0.933333
78 AD9 0.470085 0.881579
79 SAP 0.470085 0.858974
80 RBY 0.470085 0.894737
81 AGS 0.470085 0.858974
82 ADV 0.470085 0.894737
83 AU1 0.469565 0.881579
84 ADX 0.469565 0.817073
85 YAP 0.46875 0.933333
86 1ZZ 0.468254 0.851852
87 3OD 0.468254 0.932432
88 8ID 0.466667 0.897436
89 NBP 0.465753 0.897436
90 50T 0.465517 0.868421
91 OAD 0.464 0.932432
92 9ZD 0.463415 0.896104
93 9ZA 0.463415 0.896104
94 8QN 0.463415 0.945205
95 6YZ 0.46281 0.881579
96 ANP 0.462185 0.881579
97 T99 0.462185 0.87013
98 TAT 0.462185 0.87013
99 DQV 0.462121 0.945205
100 M24 0.461538 0.886076
101 PRX 0.461538 0.857143
102 NJP 0.460432 0.933333
103 PR8 0.460317 0.8625
104 NGD 0.459854 0.897436
105 A1R 0.459677 0.848101
106 AMO 0.459677 0.92
107 PAJ 0.459677 0.873418
108 B5Y 0.457364 0.933333
109 PTJ 0.456693 0.884615
110 ATF 0.454545 0.87013
111 DZD 0.453901 0.873418
112 9X8 0.452381 0.883117
113 9JJ 0.450617 0.875
114 IOT 0.449275 0.821429
115 Z5A 0.44898 0.833333
116 LAD 0.448819 0.873418
117 TYM 0.448529 0.945946
118 A3R 0.448 0.848101
119 LAQ 0.447761 0.851852
120 G A A A 0.446809 0.909091
121 A G 0.446809 0.921053
122 FYA 0.445312 0.893333
123 TXA 0.445312 0.92
124 ME8 0.445312 0.851852
125 NB8 0.445312 0.884615
126 AHX 0.444444 0.860759
127 U A G G 0.443662 0.921053
128 A22 0.443548 0.918919
129 MAP 0.443548 0.858974
130 PO4 PO4 A A A A PO4 0.440945 0.943662
131 4UV 0.439394 0.933333
132 TXE 0.437956 0.896104
133 LMS 0.4375 0.795181
134 ADQ 0.436508 0.932432
135 G3A 0.43609 0.884615
136 4UU 0.432836 0.933333
137 G5P 0.432836 0.884615
138 7MD 0.432836 0.851852
139 TXD 0.430657 0.896104
140 NAX 0.430657 0.8625
141 NAI 0.430657 0.896104
142 AOC 0.429825 0.810811
143 G5A 0.429752 0.770115
144 TAD 0.42963 0.85
145 F2R 0.429577 0.831325
146 5SV 0.428571 0.814815
147 25A 0.428571 0.931507
148 U A 0.427586 0.921053
149 5AS 0.42735 0.75
150 NMN AMP PO4 0.426573 0.933333
151 139 0.425532 0.8625
152 DSZ 0.425197 0.790698
153 8PZ 0.424242 0.790698
154 54H 0.424 0.77907
155 VMS 0.424 0.77907
156 JB6 0.423077 0.871795
157 BIS 0.423077 0.848101
158 9K8 0.423077 0.764045
159 AFH 0.422222 0.873418
160 XAH 0.421053 0.829268
161 8X1 0.420635 0.744444
162 TSB 0.420635 0.788235
163 5CA 0.420635 0.770115
164 4UW 0.42029 0.897436
165 6V0 0.42029 0.884615
166 25L 0.419847 0.918919
167 A5A 0.419355 0.797619
168 A A A 0.418605 0.918919
169 OMR 0.417266 0.841463
170 SSA 0.416 0.770115
171 NMN 0.415929 0.849315
172 P5A 0.415385 0.736264
173 ENQ 0.415385 0.930556
174 BT5 0.413793 0.821429
175 YLP 0.413043 0.831325
176 48N 0.413043 0.884615
177 52H 0.412698 0.770115
178 NCN 0.412281 0.805556
179 GA7 0.411765 0.87013
180 YSA 0.410448 0.790698
181 53H 0.409449 0.770115
182 GTA 0.408759 0.875
183 5CD 0.407407 0.794521
184 A4D 0.407407 0.783784
185 COD 0.406897 0.781609
186 XYA 0.40566 0.808219
187 ADN 0.40566 0.808219
188 RAB 0.40566 0.808219
189 T5A 0.405594 0.831325
190 YLA 0.405594 0.831325
191 GSU 0.40458 0.790698
192 AP0 0.404255 0.860759
193 YLB 0.404255 0.831325
194 YLC 0.404255 0.851852
195 7MC 0.404255 0.831325
196 4TC 0.404255 0.884615
197 CNV FAD 0.403614 0.833333
198 LSS 0.403101 0.752809
199 NSS 0.403101 0.790698
200 AYB 0.402778 0.821429
201 A4P 0.401408 0.811765
202 80F 0.401361 0.853659
203 FAD NBT 0.401198 0.76087
204 UP5 0.4 0.907895
205 NVA LMS 0.4 0.764045
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1KQP; Ligand: ADJ; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 1kqp.bio1) has 40 residues
No: Leader PDB Ligand Sequence Similarity
1 1XNG ATP 38.806
Pocket No.: 2; Query (leader) PDB : 1KQP; Ligand: ADJ; 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: 1kqp.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
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