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 PDD 0.605634 0.875
7 PP3 0.605634 0.875
8 IK2 0.597222 0.850746
9 TLP 0.589041 0.875
10 2BO 0.589041 0.875
11 2BK 0.589041 0.875
12 IN5 0.585714 0.84375
13 PPD 0.581081 0.920635
14 C6P 0.581081 0.920635
15 PY5 0.573333 0.893939
16 PLA 0.573333 0.893939
17 7XF 0.558442 0.921875
18 PGU 0.558442 0.921875
19 ILP 0.558442 0.848485
20 CBA 0.558442 0.835821
21 PDG 0.558442 0.921875
22 33P 0.554054 0.80303
23 QLP 0.551282 0.867647
24 PMG 0.551282 0.895522
25 PMH 0.546667 0.701299
26 76U 0.544304 0.878788
27 HEY 0.544304 0.865672
28 PY6 0.544304 0.867647
29 PXP 0.538462 0.761905
30 PSZ 0.5375 0.8
31 N5F 0.5375 0.907692
32 ORX 0.5375 0.907692
33 3LM 0.5375 0.788732
34 EA5 0.5375 0.880597
35 RW2 0.536585 0.852941
36 DCS 0.531646 0.763158
37 PE1 0.530864 0.907692
38 PMP 0.530303 0.825397
39 GT1 0.522388 0.686567
40 7TS 0.518987 0.708861
41 PL4 0.518072 0.907692
42 PXG 0.518072 0.861538
43 PL2 0.5125 0.785714
44 9YM 0.512195 0.835821
45 KAM 0.505882 0.850746
46 AQ3 0.483146 0.893939
47 PL8 0.476744 0.808219
48 7B9 0.465909 0.842857
49 PLP ALO 0.45 0.830769
50 PLP 2KZ 0.444444 0.80303
51 PPG 0.443182 0.850746
52 LCS 0.440476 0.705128
53 PLR 0.432836 0.671875
54 CAN PLP 0.425287 0.838235
55 GLY PLP 0.423077 0.753846
56 1D0 0.419355 0.852941
57 PLP 0.414286 0.714286
58 AN7 0.410256 0.71875
59 PZP 0.408451 0.71875
60 0LD 0.405941 0.625
61 FOO 0.405063 0.753846
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: 109
This union binding pocket(no: 1) in the query (biounit: 1j0d.bio2) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4PXE GLV 0.02677 0.40765 1.46628
2 1Y63 ADP 0.01156 0.41999 1.63043
3 1XP8 AGS 0.03347 0.40045 1.63934
4 2CBZ ATP 0.004511 0.45556 1.68776
5 4KCT FDP 0.00478 0.4347 1.75953
6 2DVZ GLU 0.002965 0.44953 1.91083
7 3MA0 XYP 0.02904 0.40944 1.91693
8 1Q8S MAN MMA 0.02587 0.4083 1.98413
9 4CCW VKC 0.01313 0.41761 2.00669
10 1V8K ANP 0.009173 0.42503 2.05279
11 4P83 U5P 0.007239 0.43017 2.1978
12 3DC4 ADP 0.03311 0.40466 2.34604
13 2JKY 5GP 0.007932 0.41999 2.34742
14 3B5J 12D 0.01217 0.42769 2.46914
15 3NHB ADP 0.02658 0.41189 2.61438
16 5FJJ MAN 0.0271 0.41677 2.6393
17 1G6H ADP 0.004992 0.45268 2.72374
18 3FIU POP 0.01617 0.42341 2.81124
19 2F5X ASP 0.007794 0.43788 2.88462
20 2OG2 MLI 0.006804 0.45209 2.93255
21 4B2D FBP 0.002922 0.43645 2.93255
22 3VC3 C6P 0.0009819 0.42127 2.93255
23 2WVZ KIF 0.01137 0.41633 2.93255
24 3BMQ AX5 0.03427 0.40812 2.93255
25 3UIE ANP 0.01977 0.40101 3
26 5B3A 0JO 0.0008613 0.41226 3.22581
27 1GOJ ADP 0.0334 0.40819 3.22581
28 4IEE AGS 0.02901 0.40368 3.22581
29 4IVN BMX 0.01468 0.40042 3.23741
30 3B9Q MLI 0.01607 0.43121 3.31126
31 2AWN ADP 0.006934 0.4501 3.51906
32 2NCD ADP 0.03203 0.40739 3.51906
33 2PS1 ORO 0.001772 0.46599 3.53982
34 2PS1 PRP 0.01042 0.40083 3.53982
35 1XTT U5P 0.00479 0.42644 3.7037
36 3BY9 SIN 0.004349 0.45558 3.84615
37 3RGQ 5P5 0.03227 0.40708 3.84615
38 1G8S MET 0.006297 0.44553 3.91304
39 3N29 GOL 0.01203 0.42591 4.10557
40 2H92 C5P 0.02074 0.40351 4.10959
41 2GZM DGL 0.02627 0.40207 4.11985
42 1JI0 ATP 0.01943 0.41695 4.16667
43 3RC3 ANP 0.02152 0.41038 4.39883
44 3W5J GDP 0.01205 0.42813 4.41176
45 5EYW PGA 0.02913 0.40358 4.41767
46 1TV5 ORO 0.02868 0.40921 4.51467
47 1YOE RIB 0.01039 0.42667 4.65839
48 2VQO TFG 0.03391 0.40016 4.69208
49 3F81 STT 0.02104 0.4068 4.91803
50 2Z4T LBT 0.01161 0.43606 4.98534
51 4WA2 SIA GAL NAG 0.03431 0.40384 4.98534
52 5AVF TAU 0.01851 0.41376 5.05837
53 1PZM 5GP 0.008231 0.43185 5.21327
54 4PPF FLC 0.001585 0.48171 5.27859
55 4B1L FRU 0.01247 0.41384 5.45455
56 3WIR BGC 0.02993 0.40317 5.57185
57 4QYS PLR 0.0002165 0.50014 5.8651
58 4QYS PLP SEP 0.00002649 0.4946 5.8651
59 2FYF PLP 0.02441 0.40756 5.8651
60 4AG5 ADP 0.03923 0.40169 5.8651
61 1MZV AMP 0.008715 0.42614 5.95745
62 5JSQ 6MS 0.005933 0.43012 6.01852
63 2AJH MET 0.02168 0.41648 6.12245
64 1N5S ADL 0.01762 0.40001 6.25
65 1VHW ADN 0.01986 0.40819 6.32411
66 2C5S AMP 0.01449 0.41924 6.45161
67 2X2T GAL NGA 0.02276 0.42427 6.53595
68 1YQT ADP 0.008411 0.438 6.74487
69 2BES RES 0.02128 0.40297 6.97674
70 1ECC PCP 0.002786 0.41589 7.03812
71 4K7O EKZ 0.02516 0.40982 7.14286
72 3AB4 LYS 0.0329 0.40084 7.30337
73 4CP8 MLI 0.03295 0.40703 7.33138
74 1FWV SGA MAG FUC 0.0244 0.41356 7.46269
75 1VBO MAN MAN MAN 0.03901 0.40443 8.05369
76 1JJ7 ADP 0.006472 0.44553 8.07692
77 2VFK AMP 0.04542 0.40277 8.29268
78 4YDS ATP 0.03133 0.40594 8.33333
79 4JLS 3ZE 0.00177 0.47553 9.21053
80 4CIB 7UZ 0.0312 0.4079 9.38416
81 3CNL GNP 0.02418 0.40776 9.92366
82 3QH2 3NM 0.008378 0.43623 9.95475
83 3LRE ADP 0.01403 0.42612 9.97067
84 2V2G BEZ 0.02231 0.41532 10.3004
85 3LN9 FLC 0.003496 0.45405 10.7914
86 3MBI HSX 0.001013 0.47839 10.8014
87 5EW0 3C7 0.01882 0.41769 11.1111
88 2AL2 PEP 0.009054 0.42116 11.1437
89 3OEN GLU 0.0232 0.40479 11.1888
90 1DQN IMU 0.004373 0.44592 11.3043
91 4N82 FMN 0.00151 0.44551 11.7978
92 3A4M ADP 0.01582 0.42167 11.9231
93 1GPM CIT 0.03586 0.40392 12.0235
94 3W6G FLC 0.03489 0.40345 12.5
95 1GXU 2HP 0.007811 0.44727 13.1868
96 4IP7 FBP 0.00337 0.43356 13.1965
97 2JBH 5GP 0.00883 0.43029 13.7778
98 1UI0 URA 0.03024 0.40959 14.1463
99 2H88 TEO 0.01286 0.4219 14.5631
100 1HGX 5GP 0.005813 0.43959 15.3005
101 4ZBY URA 0.02975 0.40884 15.9794
102 1D6S MET PLP 0.0003687 0.42926 16.1491
103 1D6S PLP MET 0.000297 0.42836 16.1491
104 2W58 ADP 0.01455 0.4224 17.8218
105 1V7C HEY 0.000007103 0.50102 19.6581
106 5IXJ THR 0.0006003 0.43773 23.7537
107 3PC3 P1T 0.0001787 0.43154 25.2199
108 3ZEI AWH 0.0003716 0.44442 33.871
109 4D9M 0JO 0.00008509 0.48273 35.1906
Pocket No.: 2; Query (leader) PDB : 1J0D; Ligand: 5PA; 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: 1j0d.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1J0D; Ligand: 5PA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1j0d.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1J0D; Ligand: 5PA; Similar sites found: 29
This union binding pocket(no: 4) in the query (biounit: 1j0d.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2FJK 13P 0.02089 0.40573 1.96721
2 1Q8Q MAN MMA 0.02003 0.41555 1.98413
3 2GNM MAN 0.02809 0.40786 1.98413
4 3WXL ADP 0.01109 0.423 2.05279
5 2XT3 ADP 0.03148 0.40466 2.34604
6 3UEC ALA ARG TPO LYS 0.02564 0.41147 2.73973
7 1UY4 XYP XYP XYP XYP 0.04164 0.40011 2.75862
8 3PNQ 2HA 0.04067 0.40371 2.93255
9 1M3U KPL 0.006773 0.43473 3.0303
10 1I1Q TRP 0.01931 0.41144 3.125
11 5HJM HSL 0.04267 0.40174 3.22581
12 3JUC PCA 0.02885 0.4095 3.26797
13 5BU2 AMP 0.01381 0.41635 3.51906
14 1ZUW DGL 0.02572 0.40504 4.04412
15 3G5N PB2 0.0285 0.41084 4.10557
16 4WZ6 ATP 0.03128 0.40684 4.13793
17 5HX1 UMP 0.02764 0.40768 5.7971
18 3OPT AKG 0.03679 0.40178 7.03812
19 2VDF OCT 0.02096 0.4126 7.11462
20 4JBL MET 0.01897 0.41614 7.37463
21 4A3R CIT 0.01689 0.4029 7.62463
22 3EXS 5RP 0.02354 0.40312 8.59729
23 2B6N ALA PRO THR 0.03791 0.41323 8.99281
24 3T50 FMN 0.008994 0.40538 10.1562
25 2WDQ TEO 0.01683 0.41888 10.4348
26 2AL2 2PG 0.0104 0.41679 11.1437
27 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.02108 0.40553 13.3333
28 1N13 AG2 0.01185 0.42819 14.1593
29 3OQJ 3CX 0.02236 0.41237 14.786
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