Receptor
PDB id Resolution Class Description Source Keywords
1MBZ 2.47 Å EC: 3.-.-.- BETA-LACTAM SYNTHETASE WITH TRAPPED INTERMEDIATE STREPTOMYCES CLAVULIGERUS CLAVULANIC ACID ASPARAGINE SYNTHETASE BETA-LACTAM SYNTHETACARBOXYETHYL ARGININE DEOXYGUANIDINOPROCLAVAMINIC ACID HY
Ref.: THE CATALYTIC CYCLE OF BETA -LACTAM SYNTHETASE OBSE X-RAY CRYSTALLOGRAPHIC SNAPSHOTS PROC.NATL.ACAD.SCI.USA V. 99 14752 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:607;
B:605;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
IOT A:606;
B:603;
Valid;
Valid;
none;
none;
submit data
561.443 C18 H28 N9 O10 P c1nc(...
MG A:603;
A:604;
B:601;
B:602;
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:605;
B:604;
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
1JGT 1.95 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF BETA-LACTAM SYNTHETASE STREPTOMYCES CLAVULIGERUS BETA-LACTAM SYNTHETASE ASPARAGINE SYNTHETASE CLAVULANIC ACAMPCPP CEA CARBOXYETHYLARGININE HYDROLASE
Ref.: STRUCTURE OF BETA-LACTAM SYNTHETASE REVEALS HOW TO SYNTHESIZE ANTIBIOTICS INSTEAD OF ASPARAGINE. NAT.STRUCT.BIOL. V. 8 684 2001
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 1MC1 - PCX C9 H16 N4 O3 [H]/N=C(/N....
2 1JGT - CMA C9 H18 N4 O4 C(C[C@@H](....
3 1MB9 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 1MBZ - IOT C18 H28 N9 O10 P c1nc(c2c(n....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 176 families.
1 1MC1 - PCX C9 H16 N4 O3 [H]/N=C(/N....
2 1JGT - CMA C9 H18 N4 O4 C(C[C@@H](....
3 1MB9 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 1MBZ - IOT C18 H28 N9 O10 P c1nc(c2c(n....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 143 families.
1 1MC1 - PCX C9 H16 N4 O3 [H]/N=C(/N....
2 1JGT - CMA C9 H18 N4 O4 C(C[C@@H](....
3 1MB9 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 1MBZ - IOT C18 H28 N9 O10 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: IOT; Similar ligands found: 215
No: Ligand ECFP6 Tc MDL keys Tc
1 IOT 1 1
2 CA0 0.617647 0.833333
3 WAQ 0.607143 0.914634
4 DLL 0.589286 0.843373
5 TXA 0.587719 0.823529
6 1ZZ 0.587719 0.850575
7 5AL 0.583333 0.843373
8 SRP 0.572727 0.890244
9 OOB 0.571429 0.843373
10 A2D 0.568627 0.809524
11 AMO 0.566372 0.86747
12 YLP 0.565574 0.917647
13 LAD 0.565217 0.939024
14 YLC 0.564516 0.916667
15 AN2 0.561905 0.821429
16 00A 0.561404 0.804598
17 BA3 0.557692 0.809524
18 8QN 0.557522 0.843373
19 ADX 0.556604 0.73913
20 M33 0.556604 0.8
21 3UK 0.556522 0.833333
22 4AD 0.552632 0.857143
23 PAJ 0.552632 0.806818
24 ADP 0.552381 0.831325
25 AP5 0.552381 0.809524
26 B4P 0.552381 0.809524
27 YLB 0.552 0.917647
28 ACP 0.551402 0.833333
29 9SN 0.550847 0.795455
30 AHX 0.547826 0.837209
31 NB8 0.547009 0.837209
32 PTJ 0.547009 0.816092
33 ME8 0.547009 0.829545
34 AYB 0.546875 0.906977
35 LAQ 0.544715 0.850575
36 XAH 0.541667 0.894118
37 AD9 0.541284 0.811765
38 A 0.539216 0.829268
39 AMP 0.539216 0.829268
40 YLA 0.539062 0.917647
41 4UV 0.53719 0.813953
42 ATP 0.537037 0.831325
43 50T 0.537037 0.8
44 FA5 0.533333 0.86747
45 YAP 0.533333 0.857143
46 AQP 0.53211 0.831325
47 AR6 0.53211 0.831325
48 PRX 0.53211 0.811765
49 5FA 0.53211 0.831325
50 APR 0.53211 0.831325
51 ANP 0.531532 0.811765
52 ACQ 0.531532 0.833333
53 AGS 0.527273 0.793103
54 SAP 0.527273 0.793103
55 PR8 0.525424 0.951219
56 ABM 0.52381 0.788235
57 ATF 0.522124 0.802326
58 FYA 0.521008 0.843373
59 ARG AMP 0.52 0.951807
60 SON 0.518519 0.890244
61 GAP 0.517857 0.855422
62 5SV 0.517241 0.816092
63 OAD 0.516949 0.833333
64 4UU 0.516129 0.813953
65 AMP MG 0.514286 0.767442
66 AP2 0.514019 0.845238
67 A12 0.514019 0.845238
68 AU1 0.513761 0.811765
69 A1R 0.512821 0.891566
70 4UW 0.511811 0.786517
71 BT5 0.511278 0.885057
72 J7C 0.509434 0.829268
73 3OD 0.508333 0.833333
74 BIS 0.508333 0.825581
75 YLY 0.507353 0.906977
76 SRA 0.504762 0.790698
77 APC 0.504505 0.845238
78 NXX 0.5 0.823529
79 DND 0.5 0.823529
80 N0B 0.496403 0.917647
81 TYM 0.496124 0.86747
82 OMR 0.496124 0.840909
83 DAL AMP 0.495726 0.821429
84 A22 0.495726 0.821429
85 MYR AMP 0.491803 0.829545
86 25A 0.491525 0.831325
87 TAT 0.491228 0.802326
88 ADQ 0.487395 0.833333
89 RBY 0.486726 0.845238
90 ADV 0.486726 0.845238
91 ADP MG 0.486486 0.77907
92 MAP 0.483051 0.793103
93 BEF ADP 0.482143 0.761364
94 ADP BEF 0.482143 0.761364
95 48N 0.48062 0.858824
96 CNA 0.477612 0.823529
97 NAX 0.476923 0.818182
98 TXD 0.476923 0.825581
99 ADP PO3 0.473684 0.807229
100 G3A 0.472441 0.858824
101 COD 0.470588 0.865169
102 ATP MG 0.469565 0.77907
103 G5P 0.46875 0.858824
104 7MD 0.46875 0.916667
105 AFH 0.46875 0.806818
106 TYR AMP 0.468254 0.823529
107 25L 0.467742 0.821429
108 ANP MG 0.466102 0.772727
109 NAI 0.465649 0.784091
110 A3D 0.463768 0.811765
111 6RE 0.462963 0.819277
112 TXE 0.462121 0.825581
113 NAD 0.459854 0.821429
114 JB6 0.459677 0.825581
115 7MC 0.458647 0.895349
116 LPA AMP 0.458015 0.829545
117 ALF ADP 0.457627 0.752809
118 ADP ALF 0.457627 0.752809
119 SAH 0.456897 0.761905
120 5X8 0.45614 0.738095
121 6V0 0.454545 0.795455
122 M24 0.453901 0.777778
123 ADP VO4 0.453782 0.8
124 SSA 0.453782 0.755319
125 VO4 ADP 0.453782 0.8
126 AMP DBH 0.453125 0.770115
127 KAA 0.451613 0.806452
128 A A 0.451613 0.809524
129 GSU 0.451613 0.774194
130 DSZ 0.45082 0.755319
131 0UM 0.45082 0.8
132 GJV 0.45045 0.831325
133 139 0.448529 0.83908
134 SXZ 0.448 0.75
135 4TC 0.447761 0.795455
136 TSB 0.446281 0.715789
137 5CA 0.446281 0.755319
138 DZD 0.446043 0.848837
139 A5A 0.445378 0.723404
140 G5A 0.444444 0.774194
141 A4P 0.444444 0.853933
142 UP5 0.443609 0.793103
143 SFG 0.443478 0.768293
144 TAD 0.442748 0.806818
145 GTA 0.442748 0.829545
146 5AS 0.442478 0.736842
147 NAD IBO 0.442029 0.772727
148 FB0 0.44 0.857143
149 LSS 0.439024 0.721649
150 54H 0.438017 0.708333
151 52H 0.438017 0.701031
152 VMS 0.438017 0.708333
153 T5A 0.437956 0.811111
154 ADJ 0.437956 0.840909
155 NAQ 0.4375 0.775281
156 ATP A A A 0.4375 0.797619
157 UPA 0.437037 0.804598
158 AP0 0.437037 0.755556
159 EEM 0.436975 0.711111
160 NVA LMS 0.435484 0.721649
161 53H 0.434426 0.701031
162 YSA 0.434109 0.736842
163 2SA 0.433333 0.86747
164 AOC 0.432432 0.705882
165 ADP BMA 0.432 0.811765
166 NAE 0.430556 0.793103
167 S7M 0.429752 0.711111
168 BTX 0.428571 0.873563
169 AHZ 0.428571 0.769231
170 P5A 0.428571 0.817204
171 NAJ PYZ 0.427586 0.758242
172 NSS 0.427419 0.736842
173 5N5 0.427184 0.722892
174 PPS 0.425 0.73913
175 ZID 0.424658 0.811765
176 PAP 0.423729 0.819277
177 SA8 0.423729 0.747126
178 5CD 0.423077 0.690476
179 3DH 0.422018 0.666667
180 XYA 0.421569 0.722892
181 RAB 0.421569 0.722892
182 ADN 0.421569 0.722892
183 ARX 0.421429 0.879518
184 A3P 0.421053 0.829268
185 LEU LMS 0.420635 0.704082
186 DTA 0.420561 0.697674
187 SAI 0.420168 0.752941
188 AF3 ADP 3PG 0.419118 0.786517
189 LA8 ALF 3PG 0.419118 0.786517
190 ALF ADP 3PG 0.419118 0.786517
191 NDE 0.417219 0.823529
192 6IA 0.416667 0.827586
193 2A5 0.415254 0.855422
194 AMP NAD 0.414966 0.802326
195 A7D 0.413793 0.75
196 AR6 AR6 0.413534 0.809524
197 NDC 0.411765 0.858824
198 ATR 0.411765 0.807229
199 A4D 0.409524 0.702381
200 K15 0.409449 0.761364
201 EAD 0.409396 0.777778
202 WSA 0.408759 0.744681
203 DSH 0.40708 0.785714
204 U A G G 0.405594 0.847059
205 3AM 0.405405 0.817073
206 MTA 0.40367 0.666667
207 A3N 0.403509 0.697674
208 A2R 0.403226 0.843373
209 62X 0.401575 0.744444
210 7D5 0.4 0.797619
211 NAJ PZO 0.4 0.755556
212 4YB 0.4 0.757895
213 CMX 0.4 0.897727
214 A5D 0.4 0.697674
215 7D3 0.4 0.8
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1JGT; Ligand: APC; Similar sites found: 51
This union binding pocket(no: 1) in the query (biounit: 1jgt.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2J5V PCA 0.006828 0.44291 1.3624
2 1S4P GDP 0.004394 0.44199 1.72414
3 5H5F SAM 0.00551 0.41207 2.13675
4 2WSI FAD 0.0001285 0.48635 2.28758
5 1Y42 TYR 0.03641 0.40726 2.29592
6 1RYD GLC 0.02553 0.41759 2.32558
7 4OJ8 AKG 0.01169 0.4038 2.38908
8 3GYQ SAM 0.00824 0.41382 2.57353
9 3BBH SFG 0.005046 0.42709 2.92683
10 1TV5 ORO 0.01403 0.42945 2.93454
11 3WMX THR 0.02651 0.40016 3.07263
12 2PZ8 APC 0.0001024 0.41824 3.16901
13 3G6K FAD 0.00008231 0.46068 3.24675
14 3G6K POP 0.00006926 0.45786 3.24675
15 3RK1 ATP 0.000002082 0.43336 3.37553
16 3SHR CMP 0.01823 0.4151 3.67893
17 2DTJ THR 0.01372 0.4214 3.93258
18 3ZH4 FLC 0.04214 0.41265 4.05728
19 3OQJ 3CX 0.02934 0.40452 4.28016
20 1MXI SAH 0.004136 0.42743 4.375
21 1O97 FAD 0.002131 0.42986 4.6875
22 1O97 AMP 0.002131 0.42986 4.6875
23 1O94 AMP 0.0001022 0.40495 4.6875
24 1KQP ADJ 0.001258 0.43019 5.53506
25 4H6B 10X 0.02057 0.40868 5.64103
26 1Z82 G3P 0.04528 0.40212 5.67164
27 1Z82 G3H 0.04741 0.40103 5.67164
28 2YY8 MTA 0.005959 0.43544 5.97015
29 2YY8 SAM 0.01052 0.40586 5.97015
30 1KOR ANP 0.001433 0.45387 6.25
31 1KOR SIN 0.001391 0.45387 6.25
32 1KOR ARG 0.001391 0.45387 6.25
33 2OQ2 A3P 0.0001427 0.41506 6.89655
34 4L80 OXL 0.03031 0.41704 7.18391
35 2C5S AMP 0.00000005471 0.70568 7.21248
36 1XNG ATP 0.00004943 0.4168 7.46269
37 1K97 ASP 0.001069 0.42538 7.91209
38 1K97 CIR 0.001069 0.42538 7.91209
39 2G30 ALA ALA PHE 0.0112 0.44752 8.13953
40 4L2I FAD 0.0004163 0.43848 8.36502
41 4L2I NAD 0.0007804 0.43831 8.36502
42 5UDS ATP 0.0000001504 0.67251 9.79021
43 5WSY 7UC 0.03833 0.40216 9.82659
44 3MEH THP 0.02848 0.40162 10.4895
45 3HGM ATP 0.00007765 0.41845 10.8844
46 2B6N ALA PRO THR 0.02167 0.41729 11.8705
47 3FIU POP 0.001207 0.49078 13.253
48 3FIU AMP 0.001841 0.46566 13.253
49 1C4Q GLA GAL BGC 0.02001 0.40928 14.4928
50 1CT9 AMP 0.00000008039 0.44982 33.5283
51 1Q19 APC 0.000000002257 0.56477 35.3877
Pocket No.: 2; Query (leader) PDB : 1JGT; Ligand: CMA; Similar sites found: 47
This union binding pocket(no: 2) in the query (biounit: 1jgt.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2J5V PCA 0.006511 0.44291 1.3624
2 1S4P GDP 0.004134 0.44199 1.72414
3 2WSI FAD 0.0001181 0.48635 2.28758
4 1Y42 TYR 0.03468 0.40726 2.29592
5 1RYD GLC 0.02435 0.41759 2.32558
6 4OJ8 AKG 0.01097 0.4038 2.38908
7 3GYQ SAM 0.008236 0.41257 2.57353
8 3BBH SFG 0.004903 0.42636 2.92683
9 2PZ8 APC 0.00009867 0.42365 3.16901
10 3G6K FAD 0.0001116 0.45909 3.24675
11 3G6K POP 0.00009372 0.45879 3.24675
12 3RK1 ATP 0.000001997 0.43983 3.37553
13 3SHR CMP 0.01727 0.4151 3.67893
14 2DTJ THR 0.01582 0.41704 3.93258
15 3OQJ 3CX 0.02785 0.40452 4.28016
16 1MXI SAH 0.004063 0.42646 4.375
17 1O97 FAD 0.001914 0.43433 4.6875
18 1O97 AMP 0.001914 0.43433 4.6875
19 1O94 AMP 0.00009416 0.41105 4.6875
20 1KQP ADJ 0.001055 0.43593 5.53506
21 4H6B 10X 0.01947 0.40868 5.64103
22 1Z82 G3P 0.04528 0.40099 5.67164
23 2YY8 MTA 0.005612 0.43544 5.97015
24 2YY8 SAM 0.009864 0.40586 5.97015
25 1MJH ATP 0.0003928 0.40396 6.17284
26 1KOR SIN 0.001075 0.46137 6.25
27 1KOR ANP 0.001108 0.46137 6.25
28 1KOR ARG 0.001075 0.46137 6.25
29 2OQ2 A3P 0.0001579 0.41858 6.89655
30 4L80 OXL 0.03506 0.4134 7.18391
31 2C5S AMP 0.00000004958 0.70568 7.21248
32 1XNG ATP 0.000048 0.42176 7.46269
33 1K97 ASP 0.0009261 0.43055 7.91209
34 1K97 CIR 0.0009261 0.43055 7.91209
35 2G30 ALA ALA PHE 0.01074 0.44752 8.13953
36 4L2I FAD 0.0003267 0.44553 8.36502
37 4L2I NAD 0.0006118 0.44535 8.36502
38 5UDS ATP 0.0000001365 0.67251 9.79021
39 5WSY 7UC 0.03648 0.40216 9.82659
40 3HGM ATP 0.00007013 0.42525 10.8844
41 2B6N ALA PRO THR 0.02074 0.41729 11.8705
42 3EXS 5RP 0.02871 0.40028 12.6697
43 3FIU POP 0.001242 0.48883 13.253
44 3FIU AMP 0.001804 0.46473 13.253
45 1C4Q GLA GAL BGC 0.02812 0.40073 14.4928
46 1CT9 AMP 0.00000007296 0.45737 33.5283
47 1Q19 APC 0.000000002152 0.57428 35.3877
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