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
992.615 n/a [P+](...
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: 162
No: Ligand ECFP6 Tc MDL keys Tc
1 AMP NAD 1 1
2 NAD IBO 0.715447 0.96
3 A3D 0.712 0.959459
4 NAD 0.696 0.945946
5 NAJ PYZ 0.659091 0.8875
6 DND 0.645161 0.946667
7 NXX 0.645161 0.946667
8 N01 0.628788 0.972603
9 ADP MG 0.594595 0.92
10 BEF ADP 0.589286 0.896104
11 ADP BEF 0.589286 0.896104
12 NA0 0.585714 0.946667
13 NAQ 0.57554 0.910256
14 NAP 0.571429 0.933333
15 ZID 0.571429 0.933333
16 NHD 0.57037 0.92
17 NAE 0.568345 0.934211
18 NAJ 0.567164 0.945946
19 TAP 0.556338 0.873418
20 GAP 0.555556 0.933333
21 ADP PO3 0.551724 0.931507
22 NFD 0.550725 0.897436
23 ATP MG 0.547009 0.92
24 DAL AMP 0.545455 0.972603
25 NDC 0.540541 0.886076
26 MYR AMP 0.539683 0.876543
27 NDE 0.537415 0.921053
28 NAD BBN 0.525974 0.833333
29 NAD CJ3 0.519231 0.804598
30 NAD NDT 0.518519 0.739583
31 ANP MG 0.516393 0.884615
32 TYR AMP 0.515385 0.946667
33 CNA 0.510791 0.921053
34 ALF ADP 0.508197 0.860759
35 ADP ALF 0.508197 0.860759
36 VO4 ADP 0.504065 0.894737
37 ADP VO4 0.504065 0.894737
38 OOB 0.504 0.945946
39 LPA AMP 0.503704 0.853659
40 ATP A A A 0.496183 0.945205
41 AR6 AR6 0.492537 0.958904
42 AMP MG 0.486957 0.906667
43 AHZ 0.485294 0.876543
44 ABM 0.482759 0.881579
45 ADP BMA 0.48062 0.933333
46 WAQ 0.476923 0.873418
47 CA0 0.475 0.907895
48 ARG AMP 0.474453 0.843373
49 NAD TDB 0.473373 0.68932
50 1ZZ 0.473282 0.853659
51 00A 0.472868 0.897436
52 ADP 0.470588 0.881579
53 A2D 0.470085 0.906667
54 NDO 0.469799 0.907895
55 AMP 0.469565 0.88
56 A 0.469565 0.88
57 APC 0.467213 0.848101
58 SON 0.466667 0.896104
59 9SN 0.466165 0.886076
60 ALF ADP 3PG 0.464286 0.875
61 LA8 ALF 3PG 0.464286 0.875
62 5AL 0.464 0.945946
63 M33 0.46281 0.894737
64 NAJ PZO 0.462585 0.886076
65 A12 0.462185 0.848101
66 BA3 0.462185 0.906667
67 AP2 0.462185 0.848101
68 DLL 0.461538 0.945946
69 ACP 0.459016 0.858974
70 B4P 0.458333 0.906667
71 AP5 0.458333 0.906667
72 3UK 0.458015 0.933333
73 ACQ 0.456 0.858974
74 AMP DBH 0.455882 0.907895
75 A A 0.454545 0.906667
76 AN2 0.454545 0.87013
77 AF3 ADP 3PG 0.453901 0.875
78 4TA 0.452055 0.865854
79 YAP 0.451852 0.909091
80 FA5 0.451852 0.921053
81 AD9 0.451613 0.858974
82 3OD 0.451128 0.933333
83 AU1 0.45082 0.858974
84 8ID 0.450704 0.875
85 ATP 0.447154 0.881579
86 OAD 0.44697 0.933333
87 8QN 0.446154 0.945946
88 SRP 0.445312 0.896104
89 ANP 0.444444 0.858974
90 APR 0.443548 0.906667
91 AR6 0.443548 0.906667
92 AQP 0.443548 0.881579
93 5FA 0.443548 0.881579
94 PRX 0.443548 0.858974
95 LAQ 0.442857 0.831325
96 4AD 0.442748 0.909091
97 PAJ 0.442748 0.875
98 NBP 0.441558 0.875
99 SRA 0.440678 0.835443
100 PTJ 0.440298 0.886076
101 SAP 0.44 0.8375
102 ADV 0.44 0.871795
103 AGS 0.44 0.8375
104 RBY 0.44 0.871795
105 ADX 0.439024 0.797619
106 M24 0.437086 0.864198
107 50T 0.435484 0.846154
108 NJP 0.435374 0.909091
109 NGD 0.434483 0.875
110 TYM 0.433566 0.921053
111 TAT 0.433071 0.848101
112 PR8 0.432836 0.841463
113 G A A A 0.432432 0.886076
114 A1R 0.431818 0.82716
115 AMO 0.431818 0.896104
116 TXA 0.42963 0.921053
117 ME8 0.42963 0.853659
118 DZD 0.42953 0.851852
119 7MD 0.428571 0.831325
120 MAP 0.427481 0.8375
121 ATF 0.426357 0.848101
122 Z5A 0.425806 0.835294
123 TAD 0.425532 0.829268
124 4UV 0.42446 0.909091
125 LAD 0.422222 0.851852
126 U A G G 0.42 0.897436
127 NB8 0.419118 0.8625
128 FYA 0.419118 0.87013
129 AHX 0.41791 0.839506
130 A22 0.416667 0.894737
131 NAX 0.416667 0.841463
132 IOT 0.414966 0.802326
133 PO4 PO4 A A A A PO4 0.414815 0.917808
134 OMR 0.413793 0.843373
135 5SV 0.413534 0.817073
136 AOC 0.413223 0.789474
137 G3A 0.411348 0.8625
138 5AS 0.41129 0.752809
139 7MC 0.410959 0.833333
140 YLB 0.410959 0.833333
141 BT5 0.410596 0.802326
142 ADQ 0.410448 0.907895
143 YLP 0.409722 0.833333
144 54H 0.409091 0.781609
145 5AD 0.409091 0.739726
146 VMS 0.409091 0.781609
147 BIS 0.408759 0.82716
148 G5P 0.408451 0.8625
149 4UU 0.408451 0.909091
150 NAI 0.406897 0.873418
151 TXD 0.406897 0.873418
152 4UW 0.406897 0.898734
153 TSB 0.406015 0.790698
154 A5A 0.40458 0.8
155 TXE 0.40411 0.873418
156 COD 0.403974 0.784091
157 G5A 0.403101 0.752809
158 25A 0.402985 0.906667
159 T5A 0.402685 0.833333
160 139 0.402685 0.841463
161 48N 0.4 0.886076
162 DSZ 0.4 0.772727
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1KQP; Ligand: ADJ; 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: 1kqp.bio1) has 40 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1KQP; Ligand: ADJ; Similar sites found: 34
This union binding pocket(no: 2) in the query (biounit: 1kqp.bio1) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3DOO SKM 0.03895 0.41303 1.84502
2 1C3X 8IG 0.04803 0.41155 1.8797
3 4IRP UDP 0.04957 0.41243 1.99203
4 5MX4 HPA 0.04762 0.41248 2.21402
5 2FFU UDP 0.02299 0.40907 2.58303
6 1K97 CIR 0.003055 0.40174 2.95203
7 1K97 ASP 0.003055 0.40174 2.95203
8 3RK1 ATP 0.000495 0.49952 2.95359
9 3UDG TMP 0.01352 0.44588 3.32103
10 1Q19 APC 0.0000326 0.53055 3.69004
11 2C5S AMP 0.0003999 0.52145 3.69004
12 1U6R IOM 0.01349 0.43687 3.69004
13 4OCV ANP 0.02595 0.40359 3.69004
14 2D2F ADP 0.01641 0.43011 4
15 5UDS ATP 0.00005272 0.5616 4.05904
16 2AWN ADP 0.006532 0.45783 4.79705
17 3B9Q MLI 0.009745 0.43458 4.79705
18 5F7J ADE 0.02645 0.42901 4.79705
19 2OQ2 A3P 0.004907 0.43133 4.98084
20 3GP3 SEP 0.04796 0.40902 5.05837
21 1JGT CMA 0.001055 0.43593 5.53506
22 1JGT APC 0.001258 0.43019 5.53506
23 4P86 5GP 0.03828 0.40737 6.01093
24 4UZI IMD 0.01375 0.42164 6.64207
25 4F8L AES 0.04985 0.41214 6.89655
26 3S6X SIA GAL BGC 0.03143 0.43294 7.74908
27 3KTA AP5 0.03297 0.40436 9.24856
28 3X27 TRP 0.04609 0.41394 11.4391
29 1GPM AMP 0.000003805 0.65829 12.5461
30 2BOS GLA GAL GLC 0.0155 0.44195 16.1765
31 2BOS GLA GAL GLC NBU 0.01798 0.43625 16.1765
32 1IH7 GMP 0.01783 0.4325 18.0812
33 1XNG ATP 0.000000000009129 0.85104 38.806
34 1XNG DND 0.0000000001838 0.72685 38.806
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