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Receptor
PDB id Resolution Class Description Source Keywords
1J0D 2.2 Å EC: 4.1.99.4 ACC DEAMINASE MUTANT COMPLEXED WITH ACC WILLIOPSIS SATURNUS PLP DEPENDENT B GROUP LYASE
Ref.: REACTION INTERMEDIATE STRUCTURES OF 1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE: INSIGHT INTO PLP-DEPENDENT CYCLOPROPANE RING-OPENING REACTION J.BIOL.CHEM. V. 278 41069 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5PA A:1401;
B:1501;
C:1601;
D:1701;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
332.246 C12 H17 N2 O7 P Cc1c(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1J0D 2.2 Å EC: 4.1.99.4 ACC DEAMINASE MUTANT COMPLEXED WITH ACC WILLIOPSIS SATURNUS PLP DEPENDENT B GROUP LYASE
Ref.: REACTION INTERMEDIATE STRUCTURES OF 1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE: INSIGHT INTO PLP-DEPENDENT CYCLOPROPANE RING-OPENING REACTION J.BIOL.CHEM. V. 278 41069 2003
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1J0E - 1AC C4 H7 N O2 C1CC1(C(=O....
2 1J0D - 5PA C12 H17 N2 O7 P Cc1c(c(c(c....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1J0E - 1AC C4 H7 N O2 C1CC1(C(=O....
2 1J0D - 5PA C12 H17 N2 O7 P Cc1c(c(c(c....
3 1TZK - 2KT C4 H6 O3 CCC(=O)C(=....
4 1TZJ - A3B C4 H7 N O2 C=C[C@H](C....
5 1TZM - C2N C3 H6 Cl N O2 C([C@H](C(....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1J0E - 1AC C4 H7 N O2 C1CC1(C(=O....
2 1J0D - 5PA C12 H17 N2 O7 P Cc1c(c(c(c....
3 1TZK - 2KT C4 H6 O3 CCC(=O)C(=....
4 1TZJ - A3B C4 H7 N O2 C=C[C@H](C....
5 1TZM - C2N C3 H6 Cl N O2 C([C@H](C(....
6 4D99 - SER C3 H7 N O3 C([C@@H](C....
7 4D9E - LCS C11 H14 N3 O7 P Cc1c(c(c(c....
8 4D97 - DSN C3 H7 N O3 C([C@H](C(....
9 4D96 - 5PA C12 H17 N2 O7 P Cc1c(c(c(c....
10 4D9C - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
11 4D9B - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5PA; Similar ligands found: 63
No: Ligand ECFP6 Tc MDL keys Tc
1 5PA 1 1
2 PLG 0.632353 0.890625
3 P1T 0.628571 0.878788
4 PLS 0.611111 0.920635
5 PDA 0.605634 0.875
6 PP3 0.605634 0.875
7 PDD 0.605634 0.875
8 IK2 0.597222 0.850746
9 2BK 0.589041 0.875
10 2BO 0.589041 0.875
11 TLP 0.589041 0.875
12 IN5 0.585714 0.84375
13 C6P 0.581081 0.920635
14 PPD 0.581081 0.920635
15 PY5 0.573333 0.893939
16 PLA 0.573333 0.893939
17 ILP 0.558442 0.848485
18 7XF 0.558442 0.921875
19 PGU 0.558442 0.921875
20 CBA 0.558442 0.835821
21 PDG 0.558442 0.921875
22 33P 0.554054 0.80303
23 LPI 0.551282 0.855072
24 PMG 0.551282 0.895522
25 QLP 0.551282 0.867647
26 PMH 0.546667 0.701299
27 HEY 0.544304 0.865672
28 76U 0.544304 0.878788
29 PY6 0.544304 0.867647
30 PXP 0.538462 0.761905
31 ORX 0.5375 0.907692
32 3LM 0.5375 0.788732
33 EA5 0.5375 0.880597
34 N5F 0.5375 0.907692
35 PSZ 0.5375 0.8
36 RW2 0.536585 0.852941
37 DCS 0.531646 0.763158
38 PE1 0.530864 0.907692
39 PMP 0.530303 0.825397
40 GT1 0.522388 0.686567
41 7TS 0.518987 0.708861
42 PL4 0.518072 0.907692
43 PXG 0.518072 0.861538
44 PL2 0.5125 0.785714
45 9YM 0.512195 0.835821
46 KAM 0.505882 0.850746
47 AQ3 0.483146 0.893939
48 PL8 0.476744 0.808219
49 7B9 0.465909 0.842857
50 PLP 2KZ 0.444444 0.80303
51 PPG 0.443182 0.850746
52 LCS 0.440476 0.705128
53 RMT 0.438202 0.794118
54 PLR 0.432836 0.671875
55 1D0 0.419355 0.852941
56 PLP 0.414286 0.714286
57 AN7 0.410256 0.71875
58 PZP 0.408451 0.71875
59 0LD 0.405941 0.625
60 FOO 0.405063 0.753846
61 CAN PLP 0.404494 0.826087
62 P0P 0.402778 0.714286
63 KOU 0.402439 0.8
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1J0D; Ligand: 5PA; Similar sites found with APoc: 275
This union binding pocket(no: 1) in the query (biounit: 1j0d.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 3ZO7 K6H None
2 6BKK 308 None
3 6BKL RIM None
4 3T3Z 9PL 1.46628
5 4PXE GLV 1.46628
6 4GYS MLI 1.46628
7 3B6O TMP 1.61943
8 1Y63 ADP 1.63043
9 1XP8 AGS 1.63934
10 2CBZ ATP 1.68776
11 5XQL C2E 1.71821
12 4KCT FDP 1.75953
13 6A20 ADP 1.75953
14 1F76 ORO 1.78571
15 4ZNO SUC 1.79104
16 2DVZ GLU 1.91083
17 3MA0 XYP 1.91693
18 2FJK 13P 1.96721
19 1Q8S MAN MMA 1.98413
20 4CCW VKC 2.00669
21 5ZXD ATP 2.01465
22 3QTP 2PG 2.05279
23 1V8K ANP 2.05279
24 1R0X ATP 2.0979
25 5ETJ IM5 2.16049
26 4P83 U5P 2.1978
27 5NM7 GLY 2.25564
28 2IGA XX3 2.34604
29 4KVL PLM 2.34604
30 2HIM ASN 2.34604
31 3DC4 ADP 2.34604
32 2BO4 FLC 2.34604
33 2JKY 5GP 2.34742
34 3V0H I3P 2.35988
35 2Q8M AMP 2.40964
36 2A0W DIH 2.42215
37 3B5J 12D 2.46914
38 5LV1 78T 2.5
39 4GK9 MAN BMA MAN MAN MAN 2.50896
40 3NHB ADP 2.61438
41 5FJJ MAN 2.6393
42 3BOF HCS 2.6393
43 1G6H ADP 2.72374
44 3FIU POP 2.81124
45 6HKE MLT 2.83019
46 6HKE LMR 2.83019
47 3QPB R1P 2.83688
48 3QPB URA 2.83688
49 2F5X ASP 2.88462
50 2OG2 MLI 2.93255
51 4B2D FBP 2.93255
52 3VC3 C6P 2.93255
53 2WVZ KIF 2.93255
54 3BMQ AX5 2.93255
55 1TKU 5RP 2.94118
56 5FII PHE 2.94118
57 1RRC ADP 2.99003
58 3UIE ANP 3
59 3HQP FDP 3.22581
60 1YKJ PHB 3.22581
61 5B3A 0JO 3.22581
62 1GOJ ADP 3.22581
63 4IEE AGS 3.22581
64 4IVN BMX 3.23741
65 3KC1 2T6 3.2641
66 3E4O SIN 3.27869
67 3B9Q MLI 3.31126
68 1OIJ AKG 3.32226
69 5HWK BEZ 3.33333
70 1Y7I SAL 3.35821
71 4Z7X 3CX 3.36134
72 2AWN ADP 3.51906
73 3JU6 ARG 3.51906
74 2NCD ADP 3.51906
75 1OXV ANP 3.51906
76 2PS1 ORO 3.53982
77 2PS1 PRP 3.53982
78 3R7F CP 3.61842
79 4U00 ADP 3.68852
80 1XTT U5P 3.7037
81 1P6O HPY 3.72671
82 5NC1 NAG 3.79747
83 3GWZ SAH 3.81232
84 3K5I AIR 3.81232
85 4P86 5GP 3.82514
86 3BY9 SIN 3.84615
87 6C0B MLI 3.84615
88 3RGQ 5P5 3.84615
89 1G8S MET 3.91304
90 1ZUW DGL 4.04412
91 3N29 GOL 4.10557
92 5KL0 G16 4.10557
93 2H92 C5P 4.10959
94 2GZM DGL 4.11985
95 4WZ6 ATP 4.13793
96 3H4S ADP 4.14508
97 4FRZ ADP 4.14508
98 4BLW AMP 4.15225
99 1JI0 ATP 4.16667
100 2GQS C2R 4.21941
101 1O5Q PYR 4.2623
102 5LPG 71V 4.26829
103 5VJN IR8 4.27807
104 5JVB 2PO 4.28571
105 1QK3 5GP 4.29185
106 5TIV A3P 4.34783
107 3RC3 ANP 4.39883
108 3ACT BGC 4.39883
109 6AR9 3L4 4.41176
110 3W5J GDP 4.41176
111 5EYW PGA 4.41767
112 1TV5 ORO 4.51467
113 5ORG 6DB 4.56274
114 1YOE RIB 4.65839
115 3COB ADP 4.69208
116 5KOD IAC 4.69208
117 5A0U CHT 4.69208
118 1QW9 KHP 4.69208
119 2F6U CIT 4.70085
120 1HDC CBO 4.72441
121 3ITJ CIT 4.73373
122 3X44 PUS 4.81928
123 2VWT PYR 4.86891
124 3F81 STT 4.91803
125 2WPB ZZI 4.93421
126 2Z4T LBT 4.98534
127 4WA2 SIA GAL NAG 4.98534
128 5BYK OAQ 5.01931
129 5BYK A3P 5.01931
130 5AVF TAU 5.05837
131 1PZM 5GP 5.21327
132 4XZ3 ACP 5.21739
133 2PZE ATP 5.24017
134 4PPF FLC 5.27859
135 2VVG ADP 5.27859
136 4AVV CD 5.39216
137 4AVV GHE 5.39216
138 4B1L FRU 5.45455
139 5EO8 TFU 5.46624
140 2JK0 ASP 5.53846
141 2PTZ PAH 5.57185
142 3WIR BGC 5.57185
143 3K7S R52 5.58659
144 3MKN DNB 5.6962
145 5N17 8FK 5.7971
146 1UPF URF 5.80357
147 3N8K D1X 5.81395
148 4QYS PLR 5.8651
149 4QYS PLP SEP 5.8651
150 2FYF PLP 5.8651
151 4BJH PAL 5.8651
152 4AG5 ADP 5.8651
153 1MZV AMP 5.95745
154 2D2F ADP 6
155 4D52 GXL 6.03175
156 5XH2 NPO 6.10687
157 2AJH MET 6.12245
158 4KFU ACP 6.13208
159 5I7A 68Q 6.13497
160 4UDK BMA 6.15836
161 5CSS G3P 6.19469
162 1N5S ADL 6.25
163 1VHW ADN 6.32411
164 3L6R MLI 6.35838
165 4CQK PIO 6.38298
166 2C5S AMP 6.45161
167 1GXS DKA 6.45161
168 3FJO FMN 6.45161
169 4RHY 3QG 6.46766
170 6BYF CIT 6.47059
171 1W7F ICT 6.51466
172 2X2T GAL NGA 6.53595
173 4R2I ANP 6.66667
174 5X2N ALA 6.66667
175 6A6A DAL 6.66667
176 1YQT ADP 6.74487
177 1T5C ADP 6.74487
178 5O2J 2PO 6.95971
179 2BES RES 6.97674
180 3AQA BYH 7.03125
181 5YV5 ADP 7.03812
182 5ZA2 NXL 7.03812
183 1B4B ARG 7.04225
184 5C9J DAO 7.07071
185 4K7O EKZ 7.14286
186 3R77 QLI 7.17703
187 4WOH 4NP 7.22892
188 1B0U ATP 7.25191
189 5YRV 5AD 7.29927
190 2DTJ THR 7.30337
191 3AB4 LYS 7.30337
192 4CP8 MLI 7.33138
193 1PDZ PGA 7.33138
194 3WW2 SF9 7.42188
195 1FWV SGA MAG FUC 7.46269
196 2Y65 ADP 7.62463
197 2GKS ADP 7.62463
198 1VBO MAN MAN MAN 8.05369
199 1JJ7 ADP 8.07692
200 6EBQ FMN 8.125
201 4JEJ 1GP 8.19672
202 2VFK AMP 8.29268
203 4YDS ATP 8.33333
204 3B8I OXL 8.36237
205 3MMH SME 8.38323
206 2FUE M1P 8.39695
207 1C5C TK4 8.41121
208 5X7Q GLC GLC GLC 8.79765
209 5X7Q GLC GLC GLC GLC 8.79765
210 5FAW CHT 8.79765
211 1XX6 ADP 8.90052
212 5E5U MLI 9.04523
213 4JLS 3ZE 9.21053
214 4V1F BQ1 9.30233
215 4CIB 7UZ 9.38416
216 1O5O U5P 9.50226
217 6GPC ARG 9.52381
218 5TSH ADP 9.67742
219 3CNL GNP 9.92366
220 3QH2 3NM 9.95475
221 3LRE ADP 9.97067
222 2V2G BEZ 10.3004
223 2I6U NVA 10.7492
224 3LN9 FLC 10.7914
225 3MBI HSX 10.8014
226 3ACC 5GP 11.0497
227 5EW0 3C7 11.1111
228 2AL2 PEP 11.1437
229 2AL2 2PG 11.1437
230 1LVW TYD 11.1864
231 3OEN GLU 11.1888
232 1DQN IMU 11.3043
233 2BTM PGA 11.5079
234 2J5V PCA 11.7302
235 4N82 FMN 11.7978
236 3A4M ADP 11.9231
237 1GPM CIT 12.0235
238 1F9V ADP 12.1037
239 1P19 IMP 12.2172
240 4MUS LY0 12.3223
241 6GAQ FMN 12.3377
242 3W6G FLC 12.5
243 3F6R FMN 12.8378
244 1GXU 2HP 13.1868
245 4IP7 FBP 13.1965
246 1BG2 ADP 13.2308
247 4YMU ATP 13.6364
248 2JBH 5GP 13.7778
249 1UI0 URA 14.1463
250 5LJI FMN 14.1892
251 2H88 TEO 14.5631
252 2KIN ADP 15
253 1HGX 5GP 15.3005
254 1XXA ARG 15.3846
255 1D6S MET PLP 16.1491
256 1D6S PLP MET 16.1491
257 5D85 P1T 16.5644
258 5D85 FLC 16.5644
259 4QM7 GTP 17.5439
260 4WOP CTP 17.7778
261 4HEQ FMN 17.8082
262 2W58 ADP 17.8218
263 3OZG SSI 18
264 1V7C HEY 19.6581
265 6AMI TRP 23.1672
266 6AM8 PLT 23.4604
267 6AM8 TRP 23.4604
268 6CUZ FEV 23.7537
269 5TCI MLI 23.7537
270 3PC3 P1T 25.2199
271 1CX9 NHP 25.5132
272 2NZU BG6 32.9545
273 3ZEI AWH 33.871
274 4D9M 0JO 35.1906
275 6C2Z P1T 36.9501
Pocket No.: 2; Query (leader) PDB : 1J0D; Ligand: 5PA; Similar sites found with APoc: 37
This union binding pocket(no: 2) in the query (biounit: 1j0d.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 3NB0 G6P 1.75953
2 1T9D 1MM 1.75953
3 1T9D P25 1.75953
4 1T9D PYD 1.75953
5 1T9D FAD 1.75953
6 3WXL ADP 2.05279
7 6HDT BTN 2.25564
8 5AHN IMP 2.34604
9 2QGI UDP 2.41935
10 5WBF LAC 2.59259
11 3ZDS HMQ 2.6393
12 4PU5 ANP 2.93255
13 2UXR ICT 2.93255
14 5WHU SIA GAL GLC 3.3557
15 3EW2 BTN 3.7037
16 4XFR CIT 3.81232
17 3GL0 HXX 4.10557
18 5OUH L0B 4.39024
19 5Z49 RUB 4.60251
20 6FYZ EBE 4.69208
21 3CL7 HYN 5.19481
22 1OGO BGC GLC 5.27859
23 4D52 GIV 6.03175
24 1GXS BEZ 6.45161
25 5BOE PEP 7.03812
26 3HRD NIO 7.87879
27 2B6N ALA PRO THR 8.99281
28 1Y1A GSH 9.28962
29 6AYU F6P 9.38416
30 2JFQ DGL 9.44056
31 3T50 FMN 10.1562
32 2HVW DDN 10.8696
33 1GPM AMP 12.0235
34 4CSD MFU 12.5
35 1N13 AG2 14.1593
36 3OQJ 3CX 14.786
37 6F7X MFU 30
Pocket No.: 3; Query (leader) PDB : 1J0D; Ligand: 5PA; Similar sites found with APoc: 34
This union binding pocket(no: 3) in the query (biounit: 1j0d.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 5SWI BMA 1.75953
2 1A99 PUT 1.75953
3 2ZBL BMA 1.75953
4 1H82 FAD 1.75953
5 1H82 GZZ 1.75953
6 5GS9 ARG 1.78042
7 6B2W AG2 2.1021
8 5KBE IPH 2.62009
9 4CCK OGA 2.6393
10 3JQ7 DX2 2.93255
11 3MBC NAP 3.22581
12 3BJE R1P 3.22581
13 5OSW DIU 3.22581
14 2XIG CIT 3.33333
15 5BU2 AMP 3.51906
16 5DM1 5D7 3.74532
17 4Y0X ADP 3.81232
18 3K0T BGC 4.1958
19 3UXL CFI 4.39883
20 6FU4 HSM 5.57185
21 1EQ2 ADQ 5.80645
22 1W9W BGC BGC BGC GLC BGC BGC 6.33803
23 5LQ8 GB 6.73759
24 5AE2 FAD 6.74487
25 5AE2 FYC 6.74487
26 5W10 CMP 8.20513
27 4ZCW 4NG 8.5044
28 1DCP HBI 9.61539
29 5GVR LMR 13.2479
30 2P5B OGA 13.6364
31 6C8X BVR 14.1414
32 4NPT 017 14.1414
33 2QQC AG2 26.4151
34 5FWE OGA 33.3333
Pocket No.: 4; Query (leader) PDB : 1J0D; Ligand: 5PA; Similar sites found with APoc: 42
This union binding pocket(no: 4) in the query (biounit: 1j0d.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 1MJT ITU 1.75953
2 4DCT GDP 1.75953
3 1Q8Q MAN MMA 1.98413
4 1UKG MMA 1.98413
5 2GNM MAN 1.98413
6 3TTM PUT 2.05279
7 5YRF GLC GLC 2.11268
8 2XT3 ADP 2.34604
9 3UEC ALA ARG TPO LYS 2.73973
10 1UY4 XYP XYP XYP XYP 2.75862
11 1A8S PPI 2.9304
12 5NCB JZ3 2.93255
13 3PNQ 2HA 2.93255
14 3JQG AX6 2.93255
15 1I1Q TRP 3.125
16 5HJM HSL 3.22581
17 3JUC PCA 3.26797
18 3ZW2 NAG GAL FUC 3.44828
19 2R68 SUP 3.51906
20 2ZE3 AKG 3.63636
21 2YBP 2HG 4.10557
22 3G5N PB2 4.10557
23 1EWK GLU 4.10557
24 5L2R MLA 4.10557
25 5N0L ILE 4.40252
26 5G6U TRP 4.5977
27 4WOE 3S5 5.27859
28 5HX1 UMP 5.7971
29 2Q8E OGA 5.8651
30 4YMZ 13P 5.9761
31 1VBH PEP 6.15836
32 5I8F ML1 6.66667
33 3OPT AKG 7.03812
34 2VDF OCT 7.11462
35 4JBL MET 7.37463
36 4A3R CIT 7.62463
37 3EXS 5RP 8.59729
38 2ZFZ ARG 8.86076
39 4NTO 1PW 9.66184
40 2WDQ TEO 10.4348
41 4P5E N6P 11.8421
42 5O2Z FLC 12.605
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