Receptor
PDB id Resolution Class Description Source Keywords
4P87 2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF EST-Y29, A NOVEL PENICILLIN-BINDING PRO LACTAMASE HOMOLOG FROM A METAGENOMIC LIBRARY METAGENOME HYDROLASE PENICILLIN-BINDING PROTEIN BETA-LACTAMASE METAG
Ref.: CRYSTALLOGRAPHIC ANALYSIS AND BIOCHEMICAL APPLICATI NOVEL PENICILLIN-BINDING PROTEIN/ BETA-LACTAMASE HO FROM A METAGENOMIC LIBRARY. ACTA CRYSTALLOGR.,SECT.D V. 70 2455 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
4NP A:401;
B:401;
Valid;
Valid;
none;
none;
submit data
219.089 C6 H6 N O6 P c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4P87 2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF EST-Y29, A NOVEL PENICILLIN-BINDING PRO LACTAMASE HOMOLOG FROM A METAGENOMIC LIBRARY METAGENOME HYDROLASE PENICILLIN-BINDING PROTEIN BETA-LACTAMASE METAG
Ref.: CRYSTALLOGRAPHIC ANALYSIS AND BIOCHEMICAL APPLICATI NOVEL PENICILLIN-BINDING PROTEIN/ BETA-LACTAMASE HO FROM A METAGENOMIC LIBRARY. ACTA CRYSTALLOGR.,SECT.D V. 70 2455 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 4P87 - 4NP C6 H6 N O6 P c1cc(ccc1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 4P87 - 4NP C6 H6 N O6 P c1cc(ccc1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 4P87 - 4NP C6 H6 N O6 P c1cc(ccc1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 4NP; Similar ligands found: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 4NP 1 1
2 B4N 0.714286 0.866667
3 PNP 0.694444 0.906977
4 GWM 0.527778 0.619048
5 NCH 0.520833 0.629032
6 4NS 0.487179 0.76
7 BPM 0.461538 0.613636
8 NPE 0.45283 0.716981
9 HPS 0.432432 0.634146
10 PGG 0.423729 0.625
11 NPO 0.416667 0.756098
12 PNE 0.403226 0.655738
13 PDE 0.403226 0.655738
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4P87; Ligand: 4NP; Similar sites found: 270
This union binding pocket(no: 1) in the query (biounit: 4p87.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.009028 0.46187 None
2 2BJK NAD 0.002963 0.40782 1.24688
3 4FR3 0V4 0.0005797 0.44266 1.28205
4 4FR3 LYS ARG ARG LYS SEP VAL 0.0005797 0.44266 1.28205
5 1RRC ADP 0.00002161 0.42785 1.3289
6 2GN2 C5P 0.00181 0.4152 1.46199
7 4KQL 1SG 0.0007599 0.43355 1.49626
8 4HZX G39 0.0004839 0.42125 1.54639
9 2GGH NLQ 0.00003589 0.40143 1.6
10 1N6B DMZ 0.00001673 0.46465 1.74564
11 4LCQ URQ 0.00001566 0.45247 1.74564
12 4M5P MLA 0.02997 0.42443 1.74564
13 1JQN DCO 0.00001671 0.41963 1.74564
14 4LHM AZZ 0.0108 0.41598 1.74564
15 3CXO 1N5 0.0003332 0.41573 1.74564
16 3CXO 3LR 0.0004942 0.40751 1.74564
17 4HE2 AMP 0.00009478 0.40873 1.77515
18 3TO7 COA 0.001246 0.40712 1.81159
19 3CKZ ZMR 0.0004004 0.42615 1.81818
20 4EKV BTN 0.00004667 0.44484 1.88679
21 2NLI FMN 0.0001058 0.45343 1.90217
22 2NLI LAC 0.0001058 0.45343 1.90217
23 1MVN PCO 0.005455 0.40126 1.91388
24 3M0J OAF 0.00008835 0.43323 1.9544
25 1SS4 GSH 0.008541 0.45994 1.96078
26 1TV5 ORO 0.00007815 0.46722 1.99501
27 1RY2 AMP 0.0001575 0.41625 1.99501
28 4HPP GLU 0.001317 0.40281 1.99501
29 3ZPG 5GP 0.02071 0.42594 2.09424
30 1Y0G 8PP 0.04341 0.41276 2.09424
31 1SAZ ACP 0.000248 0.45891 2.09974
32 3LTW HLZ 0.004546 0.43869 2.14286
33 4CMF PXG 0.0001098 0.4529 2.17391
34 3P7I P7I 0.001753 0.44505 2.18069
35 1LTH NAD 0.00007596 0.46018 2.19436
36 1GSA ADP 0.0001585 0.44562 2.21519
37 1GSA GSH 0.0002655 0.43185 2.21519
38 3A8U PLP 0.0003457 0.40211 2.22717
39 1JXZ BCA 0.03943 0.40186 2.23048
40 1V5F FAD 0.002367 0.44786 2.24439
41 1V5F TPP 0.002367 0.44786 2.24439
42 4DYO SD4 0.009275 0.40917 2.24439
43 2C9O ADP 0.00009723 0.40404 2.24439
44 3K37 BCZ 0.00286 0.4217 2.267
45 1WL4 COA 0.001069 0.41462 2.267
46 2QCX PF1 0.009181 0.41914 2.28137
47 3HPF GAE 0.0005243 0.41524 2.30179
48 1E4E ADP 0.003093 0.40301 2.33236
49 3SHR CMP 0.008419 0.40647 2.34114
50 4DA6 GA2 0.0006037 0.43208 2.37154
51 1ZK4 AC0 0.00003698 0.48932 2.39044
52 1ZK4 NAP 0.00003698 0.48932 2.39044
53 4NVP 7CH 0.0001128 0.43595 2.39234
54 1G0N PHH 0.02294 0.42817 2.4735
55 1G0N NDP 0.02104 0.42749 2.4735
56 2BNF UTP 0.0002224 0.4307 2.48963
57 2R7K AMZ 0.002096 0.43459 2.49307
58 2R7K ACP 0.002096 0.43459 2.49307
59 4A3R CIT 0.00003754 0.45078 2.49377
60 1WDA BAG 0.01293 0.40312 2.49377
61 4K30 NLG 0.005651 0.41349 2.5
62 1J2Z SOG 0.00196 0.41601 2.59259
63 4IAE 1DX 0.002953 0.40538 2.6455
64 3G35 F13 0.01206 0.42028 2.6616
65 2NZ2 ASP 0.000009081 0.54335 2.74314
66 1AJS PLA 0.01429 0.41967 2.74314
67 2NZ2 CIR 0.000167 0.41823 2.74314
68 2A0W DIH 0.001113 0.40318 2.76817
69 1SAY PYR 0.007127 0.42289 2.77008
70 1F1V DHY 0.009933 0.40792 2.78638
71 1QDS PGA 0.01049 0.40258 2.78884
72 1SQ5 PAU 0.01338 0.407 2.92208
73 1O6B ADP 0.00008756 0.45075 2.95858
74 1RM4 NDP 0.0001543 0.4554 2.96736
75 3QV9 QV7 0.009581 0.41831 2.99252
76 4G1V FAD 0.006464 0.4169 3.00752
77 1CR1 TTP 0.001097 0.4324 3.04054
78 2JEN GLC GLC BGC XYS BGC XYS 0.004883 0.4118 3.06513
79 2RDT FMN 0.00001813 0.48288 3.10078
80 2X61 NGA GAL SIA 0.00007604 0.46398 3.10078
81 2X61 CH 0.00001435 0.46056 3.10078
82 2RDT 2RD 0.001493 0.42642 3.10078
83 1YOE RIB 0.0001049 0.42769 3.10559
84 3Q2I HP7 0.001194 0.42688 3.10734
85 3VOZ 04A 0.00007363 0.46541 3.1746
86 1Y0L HAN 0.02125 0.42886 3.24074
87 1YBH FAD 0.0008869 0.44429 3.2419
88 3UCL NAP 0.02742 0.44045 3.2419
89 3UCL CYH 0.02562 0.44045 3.2419
90 4OYA 1VE 0.002751 0.43176 3.2419
91 1V8K ANP 0.0001656 0.40147 3.2419
92 2P8B NSK 0.0007685 0.45483 3.25203
93 1W7F ICT 0.0019 0.44002 3.25733
94 4TMK T5A 0.002919 0.43485 3.28639
95 3LZW FAD 0.002071 0.40016 3.31325
96 2Z9V PXM 0.007775 0.41719 3.31633
97 4MWV BCZ 0.00009283 0.44133 3.35052
98 1XMV ADP 0.0004617 0.43328 3.37079
99 1C3M MAN MAN 0.00001683 0.40666 3.40136
100 2FR6 CTN 0.003424 0.40145 3.42466
101 4TSK NDP 0.00005624 0.46838 3.42857
102 2W41 ADP 0.004918 0.42794 3.49127
103 1FA2 DOM 0.0002101 0.41865 3.49127
104 3CQ5 PMP 0.001369 0.44386 3.52304
105 1DXY NAD 0.005094 0.41921 3.6036
106 1DXY COI 0.0001377 0.41721 3.6036
107 3QVL 5HY 0.0002599 0.44153 3.67347
108 1FW1 GSH 0.006564 0.40247 3.7037
109 1ME8 RVP 0.00009505 0.4749 3.74065
110 2QS8 MET 0.00005046 0.43723 3.74065
111 3OIG IMJ 0.000008009 0.46834 3.7594
112 3OIG NAD 0.0002886 0.44621 3.7594
113 2JFV FLC 0.01135 0.42034 3.78007
114 2Q09 DI6 0.01128 0.4056 3.84615
115 1PEA ACM 0.04339 0.40331 3.8961
116 1V6A TRE 0.008126 0.4215 3.91566
117 2BGM NAJ 0.0004707 0.43739 3.95683
118 2BGM MAX 0.00004994 0.42741 3.95683
119 4AF0 IMP 0.00001807 0.47645 3.99003
120 2YYJ 4HP 0.00009708 0.47593 3.99003
121 2YYJ FAD 0.00009708 0.47593 3.99003
122 1Q3Q ANP 0.00005831 0.46785 3.99003
123 4IVG ANP 0.0003291 0.4372 3.99003
124 4AF0 MOA 0.0004097 0.40036 3.99003
125 3P3N AKG 0.001654 0.4589 4.01146
126 1T26 GBD 0.001632 0.43802 4.03727
127 1T26 NAI 0.001632 0.43802 4.03727
128 2Y7P SAL 0.01427 0.40579 4.12844
129 2HMT NAI 0.00001532 0.4788 4.16667
130 3IU9 T07 0.0009534 0.42789 4.16667
131 2XD9 XD9 0.001551 0.45269 4.19162
132 3NOJ PYR 0.00062 0.46779 4.20168
133 1P4C FMN 0.00007601 0.47085 4.21053
134 1XX4 BAM 0.0006718 0.46626 4.21456
135 4MOB ADP 0.002621 0.41139 4.21687
136 3BY8 MLT 0.01963 0.41472 4.22535
137 1X1T NAD 0.0007677 0.43911 4.23077
138 2EJU SAH 0.002999 0.40348 4.2328
139 3S9K CIT 0.04126 0.41735 4.23729
140 1JCM 137 0.0006071 0.40483 4.2471
141 1LDM NAD 0.00007848 0.46874 4.25532
142 3K9W ADE 0.0005536 0.45549 4.27807
143 3K9W 4PS 0.0005536 0.45549 4.27807
144 2ZI8 SDT 0.00004823 0.43782 4.33333
145 1G8S MET 0.0008207 0.47291 4.34783
146 4B7J G39 0.0001568 0.42868 4.48878
147 3HU3 AGS 0.001293 0.42571 4.48878
148 4M51 BEZ 0.0189 0.42144 4.48878
149 4G87 UD1 0.001376 0.41353 4.48878
150 1Y42 TYR 0.002792 0.43636 4.59184
151 1QO0 BMD 0.01845 0.41058 4.59184
152 3ZZS TRP 0.00001222 0.4659 4.61538
153 4KS1 2H8 0.0003244 0.4313 4.61538
154 2Y6P CTP 0.01185 0.40044 4.70085
155 1A5Z OXM 0.0000171 0.57231 4.70219
156 1A5Z FBP 0.0004285 0.42883 4.70219
157 2WSB NAD 0.02374 0.42646 4.72441
158 2Z5Y HRM 0.0000244 0.43321 4.73815
159 3HZS M0E 0.001739 0.40578 4.78469
160 1G6O ADP 0.00107 0.42379 4.84848
161 1EXB NDP 0.0002426 0.45647 4.85437
162 2EB5 OXL 0.01556 0.41401 4.86891
163 3QDY CBS 0.02186 0.41247 4.8951
164 3QDY A2G GAL 0.03611 0.40734 4.8951
165 3QDT A2G GAL 0.04126 0.40441 4.8951
166 2CCV A2G 0.0003085 0.4067 4.9505
167 1I9G SAM 0.0000136 0.47812 5
168 3PHQ KDO 0.04451 0.42712 5.06912
169 1Y75 NAG 0.0007335 0.45515 5.08475
170 1I0Z OXM 0.007184 0.44979 5.1051
171 3UXL CFI 0.00002008 0.50427 5.22193
172 2ZWS PLM 0.02794 0.43396 5.23691
173 1UGX GAL MGC 0.00006649 0.42067 5.26316
174 4N02 FNR 0.00000535 0.49838 5.32213
175 1V7R CIT 0.0423 0.41623 5.37634
176 1BDB NAD 0.00131 0.43106 5.41516
177 3DG6 MUC 0.004212 0.40983 5.44959
178 2FWP ICR 0.0001239 0.43468 5.46448
179 2FWP CIT 0.0006775 0.40637 5.46448
180 1JA9 NDP 0.001047 0.4331 5.47445
181 1JA9 PYQ 0.0001137 0.42665 5.47445
182 3TKA CTN 0.001678 0.50926 5.4755
183 2XDQ MGX 0.03987 0.41105 5.48628
184 4LTN FMN 0.0003591 0.42988 5.58376
185 4LTN NAI 0.0004805 0.42988 5.58376
186 1YBQ BDH 0.000008404 0.41785 5.64103
187 1ONX ASP 0.0002044 0.41564 5.64103
188 3RO7 TDR 0.0006929 0.45197 5.66038
189 1Y9Q MED 0.01667 0.41262 5.72917
190 4GQB 0XU 0.00002484 0.47627 5.73566
191 1GJW GLC 0.004042 0.44759 5.73566
192 1VCO GLN 0.00006462 0.43044 5.73566
193 2JBH 5GP 0.01388 0.40184 5.77778
194 3DUR KDO 0.01283 0.41264 5.78512
195 3O03 NAP 0.0000699 0.46521 5.84192
196 2JE7 XMM 0.00007536 0.42846 5.85774
197 1Z44 NPO 0.01564 0.44833 5.91716
198 4I42 1HA 0.02002 0.44418 5.96491
199 4B9E FAH 0.01732 0.41734 5.98007
200 4QIJ 1HA 0.04844 0.43051 5.98802
201 2BLE 5GP 0.00004072 0.47494 5.99455
202 2ZO9 MLI 0.0001388 0.4754 6.20438
203 3FSJ D7K 0.001123 0.43205 6.23441
204 2FOI JPA 0.009376 0.40457 6.66667
205 2TOH HBI 0.0003098 0.40523 6.70554
206 2H6B 3C4 0.0003988 0.43809 6.73317
207 3MMR ABH 0.001368 0.42021 6.73317
208 1SB8 UD2 0.0315 0.42829 6.81818
209 2Q1A 2KT 0.00001826 0.46528 6.82594
210 1T0S BML 0.01752 0.42309 6.97674
211 4JF5 FLC 0.01263 0.40757 6.99588
212 4LBP 1WG 0.0003533 0.41189 7
213 1CFV E3G 0.0007524 0.40214 7.07965
214 1FNZ A2G 0.0003091 0.42525 7.173
215 4KCF FMN 0.00006783 0.4456 7.23192
216 4KCF AKM 0.0002337 0.44209 7.23192
217 2NCD ADP 0.01306 0.4123 7.23192
218 4RJK PYR 0.01078 0.4336 7.35552
219 1RSD PSB 0.000198 0.49493 7.43802
220 2IZ1 ATR 0.006621 0.43116 7.4813
221 3MAG 3MA 0.01786 0.43666 7.49186
222 1OMZ UD2 0.00003928 0.46081 7.50853
223 4Q3S X7A 0.00001743 0.45859 7.53247
224 3H86 AP5 0.002986 0.40771 7.8125
225 2WL9 MBD 0.0007232 0.40605 7.86885
226 1KW6 BPY 0.0005589 0.43809 7.87671
227 4F4S EFO 0.01722 0.40225 7.89474
228 4JP3 CIT 0.000003975 0.47768 7.94979
229 2W24 LYS 0.0001153 0.41246 8
230 1JH7 UVC 0.0005149 0.41921 8.46561
231 1Z34 2FD 0.001982 0.41237 8.51064
232 1OTH PAO 0.0003252 0.41752 8.72274
233 2IMP NAI 0.0006084 0.44653 8.72818
234 2VKL MLT 0.03187 0.42296 8.88889
235 3UEC ALA ARG TPO LYS 0.01579 0.41927 8.90411
236 3MD0 GDP 0.01461 0.4009 9.01408
237 4IEN GDP 0.0005725 0.4003 9.20245
238 3F81 STT 0.008454 0.44613 9.28962
239 3Q3C NAD 0.00001208 0.48666 9.36455
240 3CH5 GDP 0.00002737 0.41052 9.61539
241 1OFH ADP 0.0005373 0.40065 9.67742
242 3CL7 HYN 0.0003023 0.40506 9.74026
243 1ZFJ IMP 0.0002293 0.46987 9.97506
244 43CA NPO 0.02365 0.4424 10.2564
245 2C1Q BTN 0.00003379 0.45783 10.3175
246 4I9A NCN 0.000424 0.40951 10.4167
247 1QCA FUA 0.005908 0.40523 10.7981
248 1F8F NAD 0.001042 0.42417 11.2219
249 3NGU ADP 0.001314 0.42915 11.2583
250 1BTN I3P 0.008801 0.46635 11.3208
251 2PN6 GLN 0.000485 0.44603 11.3333
252 1MZV AMP 0.01153 0.40092 11.4894
253 2B7N NTM 0.0191 0.40491 12.0879
254 1NVU GTP 0.00001626 0.48446 12.4688
255 1FS5 TLA 0.0003502 0.40956 13.1579
256 1VQ2 DDN 0.002418 0.41646 13.4715
257 3MB5 SAM 0.0001214 0.45146 13.7255
258 2BOI MFU 0.01094 0.41078 14.1593
259 1ULE GLA GAL NAG 0.003972 0.45514 14.6667
260 1O9U ADZ 0.01606 0.43168 14.8571
261 3KPE TM3 0.005153 0.43618 15.3846
262 1EDO NAP 0.001014 0.43358 16.3934
263 2V5E SCR 0.02407 0.42963 16.8317
264 3EW2 BTN 0.005863 0.4217 18.5185
265 1NU4 MLA 0.004657 0.42168 19.5876
266 2EFX NFA 0.0006007 0.47323 19.8347
267 2GJ3 FAD 0.0001037 0.43032 20
268 1YQS BSA 0.0001911 0.53191 23.7822
269 1GXS BEZ 0.005556 0.41917 25.9494
270 3HLF SIM 0.0000005223 0.49333 27.0833
Pocket No.: 2; Query (leader) PDB : 4P87; Ligand: 4NP; 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: 4p87.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback