Receptor
PDB id Resolution Class Description Source Keywords
3NZ1 1.56 Å EC: 4.1.1.48 CRYSTAL STRUCTURE OF KEMP ELIMINATION CATALYST 1A53-2 COMPLE TRANSITION STATE ANALOG 5-NITRO BENZOTRIAZOLE SULFOLOBUS SOLFATARICUS TIM BARREL KEMP ELIMINATION ENZYME LYASE
Ref.: ITERATIVE APPROACH TO COMPUTATIONAL ENZYME DESIGN. PROC.NATL.ACAD.SCI.USA V. 109 3790 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3NY A:262;
Valid;
none;
submit data
164.122 C6 H4 N4 O2 c1cc2...
SO4 A:263;
A:264;
A:265;
A:266;
A:267;
A:268;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
TLA A:269;
A:270;
A:271;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
150.087 C4 H6 O6 [C@@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3NZ1 1.56 Å EC: 4.1.1.48 CRYSTAL STRUCTURE OF KEMP ELIMINATION CATALYST 1A53-2 COMPLE TRANSITION STATE ANALOG 5-NITRO BENZOTRIAZOLE SULFOLOBUS SOLFATARICUS TIM BARREL KEMP ELIMINATION ENZYME LYASE
Ref.: ITERATIVE APPROACH TO COMPUTATIONAL ENZYME DESIGN. PROC.NATL.ACAD.SCI.USA V. 109 3790 2012
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3NZ1 - 3NY C6 H4 N4 O2 c1cc2c(cc1....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3UZ5 - 0CU C6 H3 Cl2 N3 c1c(cc(c2c....
2 3UXD - 0CU C6 H3 Cl2 N3 c1c(cc(c2c....
3 3UZJ - 0CT C6 H5 N3 c1ccc2c(c1....
4 1LBL Kd = 0.014 uM 137 C12 H18 N O9 P c1ccc(c(c1....
5 1LBF Kd = 0.014 uM 137 C12 H18 N O9 P c1ccc(c(c1....
6 1A53 - IGP C11 H14 N O6 P c1ccc2c(c1....
7 3NZ1 - 3NY C6 H4 N4 O2 c1cc2c(cc1....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3UZ5 - 0CU C6 H3 Cl2 N3 c1c(cc(c2c....
2 3UXD - 0CU C6 H3 Cl2 N3 c1c(cc(c2c....
3 3UZJ - 0CT C6 H5 N3 c1ccc2c(c1....
4 1LBL Kd = 0.014 uM 137 C12 H18 N O9 P c1ccc(c(c1....
5 1LBF Kd = 0.014 uM 137 C12 H18 N O9 P c1ccc(c(c1....
6 1A53 - IGP C11 H14 N O6 P c1ccc2c(c1....
7 3NZ1 - 3NY C6 H4 N4 O2 c1cc2c(cc1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3NY; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 3NY 1 1
2 6NT 0.5 1
3 5NI 0.42 0.926829
4 2ZM 0.411765 0.926829
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3NZ1; Ligand: 3NY; Similar sites found: 240
This union binding pocket(no: 1) in the query (biounit: 3nz1.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2GJ3 FAD 0.006605 0.43675 None
2 4RT1 C2E 0.007468 0.42203 None
3 4HIA FMN 0.04654 0.40281 None
4 2RDE C2E 0.005677 0.42206 1.19522
5 5IXJ THR 0.02928 0.41262 1.51515
6 5MJA 7O3 0.002715 0.44614 1.53257
7 2CJU PHX 0.00686 0.40522 1.76991
8 2IRY DGT 0.003002 0.44752 1.91571
9 2YNE YNE 0.02587 0.43853 1.91571
10 2YNE NHW 0.02587 0.43853 1.91571
11 3RHJ NAP 0.01643 0.4364 1.91571
12 3L9R L9Q 0.02331 0.41897 1.91571
13 3L9R L9R 0.02899 0.41139 1.91571
14 4BKJ STI 0.02181 0.40796 1.91571
15 3OQJ 3CX 0.007108 0.42067 1.94553
16 3KRR DQX 0.001593 0.50226 2.29885
17 3KRU FMN 0.01092 0.44246 2.29885
18 5J75 6GQ 0.01009 0.41496 2.29885
19 3TFJ THG 0.01637 0.41102 2.29885
20 4USF 6UI 0.0274 0.40871 2.29885
21 2OVW CBI 0.0114 0.40822 2.29885
22 4NBU CAA 0.01859 0.40002 2.4
23 3E85 BSU 0.001039 0.50279 2.53165
24 3ACL 3F1 0.0009915 0.4744 2.68199
25 3GD9 GLC BGC BGC BGC 0.002355 0.44688 2.68199
26 5LRT ADP 0.006038 0.43562 2.68199
27 4YLL 4E3 0.008261 0.43169 2.68199
28 3REU ATP 0.01083 0.4191 2.68199
29 1V7C HEY 0.02109 0.41104 2.68199
30 5BW4 SAM 0.02832 0.40837 2.68199
31 3WG3 A2G GAL NAG FUC 0.008896 0.40971 2.80899
32 5DQ8 FLF 0.005129 0.44806 2.91667
33 1P1C SAH 0.01768 0.41578 3.01508
34 2C78 PUL 0.005202 0.48032 3.06513
35 5VC5 96M 0.001843 0.47018 3.06513
36 5EW9 5VC 0.01896 0.45516 3.06513
37 5X8G S0N 0.01195 0.45132 3.06513
38 3TKI S25 0.04068 0.41159 3.06513
39 5KF6 TFB 0.02947 0.40668 3.06513
40 5KF6 FAD 0.02947 0.40668 3.06513
41 2BNJ XYP XYP AHR FER 0.03044 0.40645 3.06513
42 1JQD SAH 0.0499 0.40588 3.06513
43 1TIW TFB 0.03762 0.40532 3.06513
44 1TIW FAD 0.03762 0.40532 3.06513
45 5JZJ AN2 0.02317 0.40315 3.06513
46 4H6B 10X 0.01099 0.4123 3.07692
47 5M6M 7H8 0.007689 0.41327 3.14961
48 4B1M FRU FRU 0.006361 0.41377 3.24324
49 2WZ5 MET 0.0007099 0.41612 3.26797
50 2ABS ACP 0.02402 0.42632 3.39426
51 1JG3 VAL TYR PRO IAS HIS ALA 0.01238 0.40954 3.40426
52 5UL4 SAM 0.00363 0.44808 3.44828
53 4P5Z Q7M 0.01018 0.44393 3.44828
54 1BC5 ACE ASN TRP GLU THR PHE 0.003999 0.42906 3.44828
55 3VNM SDD 0.007538 0.41915 3.44828
56 3X0D SAH 0.02428 0.40887 3.44828
57 2WME NAP 0.02445 0.40836 3.44828
58 5LVP ATP 0.01395 0.40823 3.44828
59 4HKP 16B 0.02662 0.40224 3.44828
60 1JJE BYS 0.02306 0.40277 3.6036
61 4B1L FRU 0.001015 0.45643 3.63636
62 5C83 4YN 0.009414 0.40864 3.63636
63 2XG5 EC5 0.002537 0.43754 3.66972
64 2XG5 EC2 0.002537 0.43754 3.66972
65 4N1T 2GD 0.01752 0.42286 3.77358
66 4OYA 1VE 0.003787 0.48741 3.83142
67 2AMV BIN 0.01325 0.44979 3.83142
68 2XXP DSL 0.0237 0.44204 3.83142
69 3FYS PLM 0.005887 0.43932 3.83142
70 3ALN ANP 0.006507 0.43353 3.83142
71 5MW4 5JU 0.01835 0.42713 3.83142
72 1ADO 13P 0.01297 0.42488 3.83142
73 5JFS 6K0 0.02117 0.42085 3.83142
74 1U6R ADP 0.007952 0.42027 3.83142
75 5BYZ 4WE 0.02291 0.41652 3.83142
76 4H6Q TFB 0.02403 0.40894 3.83142
77 4H6Q FAD 0.02056 0.40894 3.83142
78 5HWV MBN 0.000601 0.46265 3.84615
79 1X1Z BMP 0.04371 0.41382 3.96825
80 5BVE 4VG 0.00212 0.49103 4.21456
81 3T4L ZEA 0.0005297 0.48769 4.21456
82 5UIU 8CG 0.002097 0.47164 4.21456
83 2B4G FMN 0.002159 0.46975 4.21456
84 5KJW 53C 0.0006752 0.46281 4.21456
85 2GU8 796 0.01801 0.43832 4.21456
86 4B7X NAP 0.01514 0.42616 4.21456
87 4IGQ THR M3L GLN 0.007262 0.42562 4.21456
88 3K00 MTT 0.01294 0.42238 4.21456
89 3APT FAD 0.01486 0.41903 4.21456
90 4CQE CQE 0.0206 0.40361 4.21456
91 3UTU 1TS 0.02686 0.41782 4.2471
92 4B7P 9UN 0.04916 0.40344 4.34783
93 1LSH PLD 0.01432 0.42068 4.38871
94 1SU2 ATP 0.0116 0.42154 4.40252
95 1EIX BMQ 0.0131 0.41757 4.4898
96 5FUI APY 0.0004036 0.45551 4.54545
97 4YZC STU 0.002253 0.48636 4.5977
98 3VZ3 NAP 0.01025 0.43733 4.5977
99 5N87 N66 0.009185 0.43667 4.5977
100 3VZ3 SSN 0.01399 0.4343 4.5977
101 4AU8 Z3R 0.007929 0.42458 4.5977
102 4NMC FAD 0.0253 0.41581 4.5977
103 4I8P NAD 0.04742 0.40509 4.5977
104 2SFP PPI 0.02059 0.40256 4.5977
105 2Z6D FMN 0.01977 0.40677 4.61538
106 1ERB ETR 0.00313 0.45635 4.91803
107 3LKJ LKJ 0.03848 0.40584 4.96454
108 5VNF VAL THR SER VAL VAL 0.001475 0.45245 4.98084
109 3E9I XAH 0.006041 0.44522 4.98084
110 1ICP FMN 0.009041 0.44438 4.98084
111 5HR5 FLC 0.01024 0.44323 4.98084
112 2I7N ACO 0.009273 0.43176 4.98084
113 2JLD AG1 0.02538 0.41525 4.98084
114 1C1X HFA 0.01066 0.41519 4.98084
115 3EPO MP5 0.01325 0.415 4.98084
116 1BW9 PPY 0.01286 0.41293 4.98084
117 3K5I ADP 0.02382 0.40079 4.98084
118 2A14 SAH 0.03737 0.40035 4.98084
119 5F6U 5VK 0.003841 0.40369 5.09554
120 5LYH 7B8 0.03672 0.4059 5.18135
121 1UYY BGC BGC 0.0004502 0.48006 5.34351
122 3G5D 1N1 0.00201 0.4897 5.36398
123 1OX5 1PR 0.004694 0.46297 5.36398
124 1M15 ARG 0.005802 0.45261 5.36398
125 1M15 ADP 0.005802 0.45261 5.36398
126 4B0T ADP 0.003884 0.4472 5.36398
127 2HK5 1BM 0.004789 0.44374 5.36398
128 3EFV NAD 0.04754 0.40059 5.36398
129 4NAE 1GP 0.01215 0.40028 5.36398
130 3JQQ A2P 0.02184 0.42492 5.37975
131 4XIZ LPP 0.03997 0.40101 5.71429
132 4QNW FMN 0.006535 0.44101 5.74713
133 4YWV SSN 0.009683 0.43753 5.74713
134 3DLG GWE 0.02686 0.43016 5.74713
135 4L3L 5FI 0.01165 0.42235 5.74713
136 4LOO SB4 0.00941 0.41958 5.74713
137 3P3G UKW 0.02673 0.41659 5.74713
138 3P3G 3P3 0.02673 0.41659 5.74713
139 1IIU RTL 0.01655 0.40781 5.74713
140 4F7E 0SH 0.02879 0.41773 6.00707
141 5U98 1KX 0.01918 0.4279 6.06061
142 5L2J 6UL 0.004597 0.47759 6.12245
143 5L2J 70E 0.00483 0.47759 6.12245
144 1OVD ORO 0.004851 0.4601 6.13027
145 1OVD FMN 0.004851 0.4601 6.13027
146 1PI5 SM2 0.03966 0.41371 6.13027
147 3OV6 MK0 0.01811 0.41331 6.13027
148 3GNI ATP 0.02743 0.40078 6.13027
149 3TTC ADP 0.02893 0.40071 6.13027
150 1N07 FMN 0.03289 0.41109 6.13497
151 1KGI T4A 0.01631 0.41879 6.29921
152 3QXV MTX 0.01461 0.41886 6.34921
153 4Q5H ANP 0.01722 0.41373 6.41026
154 4R38 RBF 0.003865 0.43897 6.42857
155 5HCY 60D 0.00238 0.48214 6.51341
156 3HKW IX6 0.01095 0.45286 6.51341
157 2PNC CLU 0.006333 0.40143 6.51341
158 5XDT ZI7 0.0008914 0.49334 6.89655
159 2RKV ZBA 0.0197 0.43258 6.89655
160 5XDT MB3 0.01096 0.42975 6.89655
161 5XDT GDP 0.008087 0.42975 6.89655
162 3IWJ NAD 0.01844 0.41001 6.89655
163 2RKV COA 0.0439 0.40897 6.89655
164 3BOF HCS 0.01094 0.4058 6.89655
165 3CBC DBS 0.007736 0.40329 7.07071
166 5MY8 RXZ 0.02823 0.41079 7.27969
167 4ZSD 7I6 0.0179 0.41134 7.31707
168 5LJB RTL 0.01232 0.41841 7.40741
169 4K3H 1OM 0.01247 0.418 7.62712
170 3IES M24 0.007027 0.44751 7.66284
171 3IX8 TX3 0.006682 0.43599 7.66284
172 5JFL NAD 0.03752 0.4101 7.66284
173 3JZ4 NAP 0.04941 0.401 7.66284
174 2P5B OGA 0.01977 0.4 7.66284
175 2QM9 TDZ 0.01464 0.41452 7.74194
176 3FW4 CAQ 0.02226 0.41259 7.86517
177 4DSU BZI 0.002812 0.41699 7.93651
178 1GAR U89 0.02322 0.41415 8.01887
179 2X2M X2M 0.003689 0.45516 8.04598
180 2QK4 ATP 0.007796 0.42337 8.04598
181 4WOE ADP 0.001922 0.41552 8.04598
182 3B6R ADP 0.01013 0.4139 8.04598
183 3G08 FEE 0.00821 0.46139 8.08081
184 2Z6I FMN 0.01689 0.4148 8.13253
185 4QYN RTL 0.01923 0.40557 8.27068
186 3QSB 743 0.01455 0.40638 8.46994
187 3R96 AMP 0.007598 0.45136 8.51064
188 3R96 ACO 0.007598 0.45136 8.51064
189 3GFZ C2E 0.01468 0.42034 8.81226
190 3CXO 1N5 0.007359 0.41893 8.81226
191 5MRH Q9Z 0.001948 0.40063 8.81226
192 1GQG DCD 0.02309 0.40672 8.85714
193 1VJY 460 0.0004111 0.51401 9.1954
194 5T67 SAH 0.02272 0.43671 9.1954
195 5T67 JHZ 0.02672 0.43671 9.1954
196 2XIQ MLC 0.01852 0.42914 9.1954
197 5H9P TD2 0.003994 0.43235 9.49367
198 5UKL SIX 0.008101 0.44506 9.67742
199 5IXH OTP 0.02982 0.42021 9.93789
200 3PE2 E1B 0.04291 0.41117 9.96169
201 5H9Y BGC BGC BGC BGC BGC 0.01471 0.40288 9.96169
202 2C6Q NDP 0.03255 0.41999 10.3448
203 2WEL K88 0.008567 0.40431 10.3448
204 5A5W GUO 0.01091 0.44259 10.6719
205 5W4W 9WG 0.001976 0.46942 10.728
206 4KBA 1QM 0.0004246 0.42453 10.728
207 1ZPT FAD 0.02359 0.42005 10.728
208 5ALC TIQ 0.01113 0.43157 11.1111
209 4GID 0GH 0.02786 0.42663 11.1111
210 1RYA GDP 0.01639 0.42313 11.25
211 4WNK 453 0.003769 0.46068 11.4943
212 5L83 ASP TRP GLU ILE VAL 0.0008242 0.47477 11.6071
213 5F7R GLC GLC 0.01627 0.40938 11.6337
214 1W8S FBP 0.001848 0.45718 11.8774
215 1PS9 FMN 0.01841 0.42044 11.8774
216 3MJY IJZ 0.03572 0.40825 11.8774
217 3MJY FMN 0.03572 0.40825 11.8774
218 5FLJ QUE 0.001706 0.46365 12.3656
219 1TT8 PHB 0.0009141 0.49465 12.8049
220 3IWD M2T 0.00751 0.40126 12.9032
221 5UR1 YY9 0.01608 0.42081 13.0268
222 3QH2 3NM 0.002904 0.40014 13.1222
223 5DYO FLU 0.002297 0.43026 13.2075
224 1UJ5 5RP 0.00441 0.43868 13.2159
225 4J6W CTP 0.04086 0.4066 13.4146
226 2P1O NLA 0.04183 0.4046 13.75
227 2P1O IHP 0.04183 0.4046 13.75
228 5IH9 6BF 0.008179 0.4541 13.7931
229 5C5H 4YB 0.00772 0.44465 13.7931
230 1VPV PLM 0.006619 0.4365 14.5594
231 2YKL NLD 0.001144 0.46495 14.8148
232 4JIQ FMN 0.02241 0.4162 15.7088
233 4JIQ 1L5 0.02241 0.4162 15.7088
234 4D1J DGJ 0.006837 0.40444 16.092
235 1CLU DBG 0.01386 0.43927 16.8675
236 3TTZ 07N 0.008619 0.42185 17.1717
237 3H0L ADP 0.002144 0.44178 18.3908
238 4TW7 37K 0.01172 0.42089 20.3125
239 2G30 ALA ALA PHE 0.00003682 0.42679 20.9302
240 4WW7 AMP 0.01885 0.41702 21.9251
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