Receptor
PDB id Resolution Class Description Source Keywords
3VC3 1.77 Å EC: 2.5.1.47 CRYSTAL STRUCTURE OF BETA-CYANOALANINE SYNTHASE K95A MUTANT GLYCINE MAX BETA-CYANOALANINE SYNTHASE TRANSFERASE
Ref.: STRUCTURE OF SOYBEAN BETA-CYANOALANINE SYNTHASE AND MOLECULAR BASIS FOR CYANIDE DETOXIFICATION IN PLANT PLANT CELL V. 24 2696 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C6P A:501;
B:501;
C:501;
D:501;
E:501;
F:501;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
352.301 C11 H17 N2 O7 P S Cc1c(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3VC3 1.77 Å EC: 2.5.1.47 CRYSTAL STRUCTURE OF BETA-CYANOALANINE SYNTHASE K95A MUTANT GLYCINE MAX BETA-CYANOALANINE SYNTHASE TRANSFERASE
Ref.: STRUCTURE OF SOYBEAN BETA-CYANOALANINE SYNTHASE AND MOLECULAR BASIS FOR CYANIDE DETOXIFICATION IN PLANT PLANT CELL V. 24 2696 2012
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3VC3 - C6P C11 H17 N2 O7 P S Cc1c(c(c(c....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3VC3 - C6P C11 H17 N2 O7 P S Cc1c(c(c(c....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1Y7L Ki = 130 nM GLY ILE ASP ASP GLY MET ASN LEU ASN ILE n/a n/a
2 3IQG Kd = 24.9 uM MET ASN TRP ASN ILE n/a n/a
3 3IQH Kd = 25.8 uM MET ASN TYR ASP ILE n/a n/a
4 3IQI Kd = 38.7 uM MET ASN GLU ASN ILE n/a n/a
5 4LMB Kd = 186 uM CYS CYS n/a n/a
6 5I7A Kd = 0.32 uM 68Q C14 H10 Cl2 N2 O3 c1cc(cc(c1....
7 5I7R Kd = 1.7 uM 68W C20 H16 N2 O3 c1ccc(cc1)....
8 5I7O Kd = 3.4 uM S16 C14 H11 Cl N2 O3 c1cc(cc(c1....
9 5I6D Kd = 8 uM AU6 C15 H14 N2 O3 Cc1ccc(cc1....
10 5IW8 Kd = 2.2 uM 6EC C20 H16 N2 O4 c1ccc(cc1)....
11 3X44 - PUS C12 H17 N4 O9 P Cc1c(c(c(c....
12 2Q3D - PDA C11 H17 N2 O7 P Cc1c(c(c(c....
13 2Q3C Ki = 5 uM ASP PHE SER ILE n/a n/a
14 3ZEI ic50 = 0.103 uM AWH C20 H16 N2 O6 S CN1C(=O)/C....
15 5D85 - P1T C11 H15 N2 O7 P Cc1c(c(c(c....
16 4IL5 - ILE C6 H13 N O2 CC[C@H](C)....
17 4JBN - SER PRO SER ILE n/a n/a
18 4JBL Kd = 0.5 mM MET C5 H11 N O2 S CSCC[C@@H]....
19 3BM5 Kd = 1.1 mM CYS C3 H7 N O2 S C([C@@H](C....
20 1D6S Kd = 78 uM MET PLP n/a n/a
21 3VC3 - C6P C11 H17 N2 O7 P S Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: C6P; Similar ligands found: 75
No: Ligand ECFP6 Tc MDL keys Tc
1 C6P 1 1
2 7XF 0.80597 0.967213
3 PLS 0.8 0.966667
4 PPD 0.787879 0.966667
5 PY5 0.776119 0.90625
6 PGU 0.753623 0.935484
7 PDG 0.753623 0.935484
8 QLP 0.742857 0.878788
9 PY6 0.732394 0.878788
10 N5F 0.722222 0.920635
11 ORX 0.722222 0.920635
12 PP3 0.716418 0.918033
13 PDA 0.716418 0.918033
14 PDD 0.716418 0.918033
15 PE1 0.712329 0.920635
16 TLP 0.695652 0.918033
17 2BO 0.695652 0.918033
18 2BK 0.695652 0.918033
19 PL4 0.693333 0.920635
20 ILP 0.680556 0.888889
21 IN5 0.671642 0.885246
22 AQ3 0.641975 0.90625
23 PLG 0.623188 0.934426
24 76U 0.618421 0.890625
25 P1T 0.597222 0.920635
26 CBA 0.592105 0.875
27 IK2 0.589041 0.890625
28 5PA 0.581081 0.920635
29 KAM 0.573171 0.861538
30 EA5 0.56962 0.892308
31 33P 0.567568 0.84127
32 PLA 0.565789 0.90625
33 PMG 0.544304 0.878788
34 HEY 0.5375 0.876923
35 PSZ 0.530864 0.835821
36 3LM 0.530864 0.850746
37 PXP 0.530303 0.8
38 PXG 0.53012 0.873016
39 PMP 0.522388 0.866667
40 PMH 0.519481 0.706667
41 PLP ALO 0.519481 0.870968
42 GT1 0.514706 0.71875
43 RW2 0.511905 0.863636
44 DCS 0.506173 0.77027
45 PL2 0.506173 0.794118
46 7TS 0.493827 0.714286
47 9YM 0.470588 0.846154
48 PL8 0.454545 0.791667
49 7B9 0.444444 0.826087
50 0JO 0.443038 0.753846
51 PLP 2KZ 0.439024 0.84127
52 KOU 0.432099 0.83871
53 PLR 0.426471 0.704918
54 PPE 0.423529 0.920635
55 PZP 0.422535 0.754098
56 PPG 0.422222 0.861538
57 PLP CYS 0.421687 0.883333
58 CAN PLP 0.420455 0.848485
59 P0P 0.416667 0.75
60 1D0 0.414894 0.863636
61 PL6 0.411765 0.793651
62 PLP 0.408451 0.75
63 4LM 0.407407 0.738462
64 Z98 0.406977 0.84375
65 GAB PLP 0.406593 0.828125
66 GBC PLP 0.406593 0.828125
67 EPC 0.405063 0.741935
68 AN7 0.405063 0.754098
69 LCS 0.402299 0.710526
70 5DK 0.402174 0.818182
71 FOO 0.4 0.790323
72 PL5 0.4 0.8125
73 GLY PLP 0.4 0.790323
74 2B6 0.4 0.697368
75 PUS 0.4 0.722222
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3VC3; Ligand: C6P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3vc3.bio3) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3VC3; Ligand: C6P; Similar sites found: 98
This union binding pocket(no: 2) in the query (biounit: 3vc3.bio3) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5C2N NAG 0.0341 0.40332 None
2 4K91 SIN 0.01354 0.42139 1.45349
3 2CIR BG6 0.02917 0.40816 1.6835
4 5TG5 JW8 0.02254 0.41373 1.74419
5 5A1S FLC 0.0387 0.40058 1.74419
6 1PZM 5GP 0.01095 0.42407 1.89573
7 3RC3 ANP 0.00521 0.44055 2.03488
8 1U1J MET 0.008828 0.43299 2.03488
9 2X5F PLP 0.01438 0.41385 2.03488
10 4FRZ ADP 0.03878 0.40128 2.03488
11 4PPF FLC 0.01735 0.4258 2.32558
12 5GJC ATP 0.0208 0.40583 2.32558
13 1GVF PGH 0.007037 0.43875 2.61628
14 4OHB 5HM 0.02074 0.40589 2.63158
15 2PS1 ORO 0.01028 0.42547 2.65487
16 2JBH 5GP 0.0005746 0.4893 2.66667
17 1XTT U5P 0.007471 0.41599 2.77778
18 3OZG SSI 0.0102 0.40969 2.8
19 2JKY 5GP 0.007144 0.4207 2.8169
20 4U00 ADP 0.01406 0.43038 2.86885
21 3BJE URA 0.0228 0.41221 2.90698
22 5FUE UV4 0.01083 0.40505 2.90698
23 1J0D 5PA 0.0009819 0.42127 2.93255
24 4JEM C5P 0.006884 0.40726 2.94118
25 5AHO TLA 0.007763 0.44493 2.97619
26 1HQL GLA MBG 0.02985 0.40428 3.11284
27 2D2F ADP 0.03911 0.40011 3.2
28 4D9C PMP 0.0004336 0.44379 3.21637
29 3KVY URA 0.03187 0.40569 3.23625
30 1QB7 ADE 0.003647 0.44353 3.38983
31 1TUU AMP 0.02537 0.40535 3.48837
32 4MUV PCG 0.01489 0.40204 3.52113
33 1MZV AMP 0.0007514 0.4776 3.82979
34 4P83 U5P 0.006834 0.42996 3.84615
35 5AOA PPI 0.01924 0.40095 3.84615
36 3F4F UMP 0.015 0.4019 4.19162
37 5GVR LMR 0.003681 0.43892 4.2735
38 1G8S MET 0.03169 0.40916 4.34783
39 1VB3 KPA 0.002489 0.46237 4.36047
40 3BF1 PAU 0.01767 0.40556 4.41767
41 3HQP FDP 0.00579 0.43355 4.65116
42 2VPY PCI 0.02719 0.40788 4.65116
43 5EXK MET 0.0335 0.40463 4.83384
44 1G6H ADP 0.03337 0.40538 5.05837
45 4RUS NAG 0.005606 0.40732 5.23256
46 3CM2 X23 0.03948 0.40004 5.38462
47 4KCT FDP 0.006899 0.42547 5.52326
48 4LWM MHO 0.02308 0.4125 5.52995
49 3B8I OXL 0.02021 0.40154 5.57491
50 1P4A PCP 0.006491 0.41517 5.61404
51 2AWN ADP 0.04404 0.40355 5.81395
52 2R5V HHH 0.02214 0.40077 5.81395
53 1O5O U5P 0.003684 0.4387 5.88235
54 1L1Q 9DA 0.005255 0.41237 5.91398
55 1CZR FMN 0.01039 0.4026 5.91716
56 1BZL FAD 0.04003 0.40444 5.96708
57 1DQN IMU 0.005483 0.43941 6.08696
58 1TE2 PGA 0.01225 0.42751 6.19469
59 2VMG MBG 0.04089 0.41415 6.36943
60 4M00 SUC 0.02674 0.40372 6.39535
61 4UP4 NAG 0.0209 0.41091 6.68605
62 4UP4 NDG 0.0209 0.41091 6.68605
63 2C3H GLC GLC 0.03147 0.40005 7.14286
64 1ZN7 HSX 0.001027 0.47086 7.22222
65 1ZN7 ADE 0.001027 0.47086 7.22222
66 1ZN7 PRP 0.006323 0.41219 7.22222
67 1OFS SUC 0.02846 0.40575 7.48663
68 1OFZ FUL 0.04392 0.40003 7.55814
69 4JZ8 CIT 0.02854 0.40818 7.57098
70 4D9M 0JO 0.0000003529 0.58039 7.84884
71 2I4O ATP 0.0219 0.4047 7.84884
72 3LN9 FLC 0.003428 0.47279 7.91367
73 2YKX AKG 0.03677 0.40239 7.95699
74 3F81 STT 0.02364 0.4008 8.19672
75 3MBI HSX 0.00189 0.46298 8.7108
76 4QYS PLP SEP 0.001003 0.42914 8.72093
77 2BES RES 0.007381 0.42404 8.72093
78 4QYS PLR 0.01018 0.41725 8.72093
79 2PZE ATP 0.04587 0.40165 8.72093
80 2WL9 MBD 0.02911 0.40767 9.18033
81 1UOU CMU 0.00469 0.42938 9.30233
82 3OBT SLB 0.01553 0.42879 9.30233
83 2GND MAN 0.0189 0.41403 9.52381
84 3ACC 5GP 0.003117 0.45192 9.94475
85 1V7C HEY 0.0000002514 0.55066 10.7558
86 2FKA BEF 0.006891 0.4439 10.8527
87 1HGX 5GP 0.003617 0.44863 11.4754
88 4JLS 3ZE 0.007709 0.44017 11.8421
89 3KIF GDL 0.01636 0.41514 13.2075
90 1G6O ADP 0.01636 0.40357 13.9535
91 4JGT PYR 0.0218 0.40785 15.1163
92 3CYQ AMU 0.02602 0.40769 15.2174
93 1ZOY UQ1 0.03252 0.40377 15.873
94 1XXA ARG 0.02931 0.40615 16.6667
95 3L6C MLI 0.0001005 0.55023 27.1386
96 3L6R MLI 0.0000035 0.63536 35.4651
97 5IXJ THR 0.00006118 0.48102 39.5349
98 5B3A 0JO 0.000000000001755 0.80196 42.1512
Pocket No.: 3; Query (leader) PDB : 3VC3; Ligand: C6P; Similar sites found: 23
This union binding pocket(no: 3) in the query (biounit: 3vc3.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5HWV MBN 0.03288 0.40214 None
2 5GWE GWM 0.02303 0.40612 2.32558
3 2REG CHT 0.01805 0.42392 2.34899
4 4MBY BGC SIA GAL 0.02384 0.40534 2.51799
5 4WXJ GLU 0.02699 0.40666 2.60223
6 3NHB ADP 0.02186 0.41344 2.61438
7 3WXL ADP 0.03901 0.40346 2.90698
8 2J0W ASP 0.0424 0.40524 3.48837
9 2Z4T C5P 0.02093 0.40428 3.77907
10 2CZL TLA 0.02344 0.41039 4.04412
11 4MDB RLT 0.03253 0.40077 4.44444
12 2JAJ D20 0.0117 0.40205 5.88235
13 3KIH GDL 0.03447 0.40105 6.18557
14 4UP4 GAL NAG 0.03955 0.40351 6.68605
15 4GNI ATP 0.01366 0.40234 6.68605
16 1C3M MAN MAN 0.0152 0.41549 6.80272
17 1O68 KIV 0.03312 0.40197 7.26744
18 2WDQ TEO 0.02816 0.40569 7.82609
19 1WHT BZS 0.03784 0.40283 8.20312
20 1D4D SIN 0.0354 0.40044 10.7558
21 3BFV ADP 0.02312 0.40212 14.0221
22 5F8F SFG 0.00805 0.41298 15.1163
23 1XXR MAN 0.02288 0.40131 19.8758
Pocket No.: 4; Query (leader) PDB : 3VC3; Ligand: C6P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3vc3.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3VC3; Ligand: C6P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 3vc3.bio2) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3VC3; Ligand: C6P; Similar sites found: 6
This union binding pocket(no: 6) in the query (biounit: 3vc3.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5O4F 8VE 0.03149 0.40051 1.93798
2 1GJW GLC 0.03038 0.40608 2.90698
3 5D2H AKG 0.01545 0.4013 3.53357
4 5NE2 DGL 0.02658 0.40106 3.59712
5 2DTJ THR 0.02678 0.40031 5.05618
6 2VZ6 FEF 0.01029 0.42111 5.11182
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