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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 (20)
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 4IL5 - ILE C6 H13 N O2 CC[C@H](C)....
16 4JBN - SER PRO SER ILE n/a n/a
17 4JBL Kd = 0.5 mM MET C5 H11 N O2 S CSCC[C@@H]....
18 3BM5 Kd = 1.1 mM CYS C3 H7 N O2 S C([C@@H](C....
19 1D6S Kd = 78 uM MET PLP n/a n/a
20 3VC3 - C6P C11 H17 N2 O7 P S Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: C6P; Similar ligands found: 79
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 LPI 0.742857 0.893939
9 QLP 0.742857 0.878788
10 PY6 0.732394 0.878788
11 N5F 0.722222 0.920635
12 ORX 0.722222 0.920635
13 PDA 0.716418 0.918033
14 PP3 0.716418 0.918033
15 PDD 0.716418 0.918033
16 PE1 0.712329 0.920635
17 2BO 0.695652 0.918033
18 TLP 0.695652 0.918033
19 2BK 0.695652 0.918033
20 PL4 0.693333 0.920635
21 ILP 0.680556 0.888889
22 IN5 0.671642 0.885246
23 AQ3 0.641975 0.90625
24 PLG 0.623188 0.934426
25 76U 0.618421 0.890625
26 P1T 0.597222 0.920635
27 CBA 0.592105 0.875
28 IK2 0.589041 0.890625
29 5PA 0.581081 0.920635
30 KAM 0.573171 0.861538
31 EA5 0.56962 0.892308
32 33P 0.567568 0.84127
33 PLA 0.565789 0.90625
34 PMG 0.544304 0.878788
35 HEY 0.5375 0.876923
36 PSZ 0.530864 0.835821
37 3LM 0.530864 0.850746
38 PXP 0.530303 0.8
39 PXG 0.53012 0.873016
40 PMP 0.522388 0.866667
41 PMH 0.519481 0.706667
42 GT1 0.514706 0.71875
43 RW2 0.511905 0.863636
44 PL2 0.506173 0.794118
45 DCS 0.506173 0.77027
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 CYS 0.439024 0.934426
52 PLP 2KZ 0.439024 0.84127
53 F0G 0.4375 0.774194
54 KOU 0.432099 0.83871
55 PLR 0.426471 0.704918
56 PPE 0.423529 0.920635
57 PZP 0.422535 0.754098
58 PPG 0.422222 0.861538
59 RMT 0.417582 0.80303
60 P0P 0.416667 0.75
61 CAN PLP 0.41573 0.835821
62 1D0 0.414894 0.863636
63 PL6 0.411765 0.793651
64 EVM 0.409639 0.825397
65 PLP 0.408451 0.75
66 4LM 0.407407 0.738462
67 Z98 0.406977 0.84375
68 FEJ 0.406977 0.765625
69 GBC PLP 0.406593 0.828125
70 GAB PLP 0.406593 0.828125
71 AN7 0.405063 0.754098
72 EPC 0.405063 0.741935
73 LCS 0.402299 0.710526
74 EQJ 0.402174 0.818182
75 5DK 0.402174 0.818182
76 2B6 0.4 0.697368
77 PUS 0.4 0.722222
78 PL5 0.4 0.8125
79 FOO 0.4 0.790323
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3VC3; Ligand: C6P; Similar sites found with APoc: 140
This union binding pocket(no: 1) in the query (biounit: 3vc3.bio3) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 5C2N NAG None
2 4K91 SIN 1.45349
3 3GWZ SAH 1.45349
4 3GXO SAH 1.45349
5 5TG5 JW8 1.74419
6 1PZM 5GP 1.89573
7 3RC3 ANP 2.03488
8 1U1J MET 2.03488
9 6APL C5P 2.03488
10 4FRZ ADP 2.03488
11 4PPF FLC 2.32558
12 5GWE GWM 2.32558
13 2REG CHT 2.34899
14 4DD8 BAT 2.40385
15 4MBY BGC SIA GAL 2.51799
16 4WXJ GLU 2.60223
17 3NHB ADP 2.61438
18 1GVF PGH 2.61628
19 4OHB 5HM 2.63158
20 2PS1 ORO 2.65487
21 2JBH 5GP 2.66667
22 1XTT U5P 2.77778
23 3OZG SSI 2.8
24 2JKY 5GP 2.8169
25 3BJE URA 2.90698
26 6GXA TB8 2.90698
27 3WXL ADP 2.90698
28 1J0D 5PA 2.93255
29 4JEM C5P 2.94118
30 5AHO TLA 2.97619
31 1QK3 5GP 3.00429
32 3BOF HCS 3.19767
33 6B2W AG2 3.19767
34 4D9C PMP 3.21637
35 3KVY URA 3.23625
36 1QB7 ADE 3.38983
37 2HIM ASN 3.48837
38 2POC BG6 3.48837
39 3ITJ CIT 3.5503
40 4GNC ASO 3.67893
41 2Z4T C5P 3.77907
42 1MZV AMP 3.82979
43 4P83 U5P 3.84615
44 6H45 QEI 4.06977
45 1Z0N BCD 4.16667
46 3F4F UMP 4.19162
47 5GVR LMR 4.2735
48 4BC5 5FX 4.27509
49 2F7A BEZ 4.31034
50 1G8S MET 4.34783
51 1VB3 KPA 4.36047
52 2DUA OXL 4.48276
53 3HQP FDP 4.65116
54 2VPY PCI 4.65116
55 4PYA 2X3 4.94186
56 1G6H ADP 5.05837
57 4R8L ASP 5.19481
58 3NB0 G6P 5.23256
59 3A0E M3M 5.45455
60 4KCT FDP 5.52326
61 3B8I OXL 5.57491
62 1P4A PCP 5.61404
63 1RZM E4P 5.6213
64 5YRL GLC GLC 5.6338
65 5YRG BGC GLC 5.6338
66 5YRJ BGC GLC 5.6338
67 1AG9 FMN 5.71429
68 5WQJ 7N3 5.81395
69 1H74 ILE 5.81395
70 3W8X FTK 5.81395
71 3W8X FAD 5.81395
72 3GD8 GOL 5.8296
73 1O5O U5P 5.88235
74 1L1Q 9DA 5.91398
75 1CZR FMN 5.91716
76 1RRC ADP 5.98007
77 1W8S FBP 6.08365
78 1DQN IMU 6.08696
79 3E81 SLB 6.09756
80 3KIH GDL 6.18557
81 1TE2 PGA 6.19469
82 2FCR FMN 6.35838
83 2VMG MBG 6.36943
84 4M00 SUC 6.39535
85 4UP4 GAL NAG 6.68605
86 4GNI ATP 6.68605
87 1C3M MAN MAN 6.80272
88 3JWH SAH 6.91244
89 6AR9 3L4 6.98529
90 4P86 5GP 7.10383
91 5KJW 53C 7.26744
92 1O68 KIV 7.26744
93 4JZ8 CIT 7.57098
94 4D9M 0JO 7.84884
95 2I4O ATP 7.84884
96 3LN9 FLC 7.91367
97 2YKX AKG 7.95699
98 2VOH CIT 8.28025
99 1P19 IMP 8.43023
100 3MBI HSX 8.7108
101 4QYS PLP SEP 8.72093
102 2BES RES 8.72093
103 4QYS PLR 8.72093
104 1TL2 NDG 8.72093
105 1B09 PC 9.2233
106 3OBT SLB 9.30233
107 2D3N GLC GLC GLC 9.30233
108 2GND MAN 9.52381
109 1Q8S MAN MMA 9.52381
110 5VJN ADE 9.62567
111 5VJN IR8 9.62567
112 3ACC 5GP 9.94475
113 3LTW HLZ 10.7143
114 1V7C HEY 10.7558
115 4USI AKG 11.039
116 1HGX 5GP 11.4754
117 3THR C2F 11.6041
118 4JLS 3ZE 11.8421
119 3KIF GDL 13.2075
120 3LLZ GAL NGA 13.5338
121 1G6O ADP 13.9535
122 3BFV ADP 14.0221
123 5F8F SFG 15.1163
124 3CYQ AMU 15.2174
125 3TL1 JRO 15.7233
126 1ZOY UQ1 15.873
127 1XXA ARG 16.6667
128 6DZN AE3 17.6991
129 5DNC ASN 17.7326
130 1CX9 NHP 22.6744
131 3L6C MLI 27.1386
132 1UPF URF 27.6786
133 3L6R MLI 35.4651
134 6AMI TRP 39.5349
135 6AM8 PLT 40.1163
136 6AM8 TRP 40.1163
137 6CUZ FEV 40.1163
138 5B3A 0JO 42.1512
139 5D85 P1T 48.773
140 6C2Z P1T 49.4186
Pocket No.: 2; Query (leader) PDB : 3VC3; Ligand: C6P; Similar sites found with APoc: 35
This union binding pocket(no: 2) in the query (biounit: 3vc3.bio3) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 2CIR BG6 1.6835
2 5A1S FLC 1.74419
3 2X5F PLP 2.03488
4 2AK3 AMP 2.65487
5 4U00 ADP 2.86885
6 1KKR 2AS 2.90698
7 2D2F ADP 3.2
8 1TUU AMP 3.48837
9 4MUV PCG 3.52113
10 5AOA PPI 3.84615
11 3BF1 PAU 4.41767
12 5EXK MET 4.83384
13 4RUS NAG 5.23256
14 3CM2 X23 5.38462
15 4LWM MHO 5.52995
16 2AWN ADP 5.81395
17 2R5V HHH 5.81395
18 1XDS SAM 6.10465
19 5JIL 6KL 6.4433
20 4UP4 NAG 6.68605
21 4UP4 NDG 6.68605
22 2C3H GLC GLC 7.14286
23 2D0O ADP 7.2
24 1OFZ FUC 7.55814
25 1OFZ FUL 7.55814
26 3F81 STT 8.19672
27 4M3P HCS 8.43023
28 2PZE ATP 8.72093
29 2WL9 MBD 9.18033
30 1UOU CMU 9.30233
31 2FKA BEF 10.8527
32 2B99 RDL 14.1026
33 4JGT PYR 15.1163
34 1C1X HFA 16.2791
35 6FLZ MMA 25
Pocket No.: 3; Query (leader) PDB : 3VC3; Ligand: C6P; Similar sites found with APoc: 20
This union binding pocket(no: 3) in the query (biounit: 3vc3.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 5HWV MBN None
2 5HC0 NPO 2.61628
3 2UVO NAG 2.92398
4 2J0W ASP 3.48837
5 5NE2 DGL 3.59712
6 2CZL TLA 4.04412
7 4MDB RLT 4.44444
8 4K6B GLU 4.96894
9 1W6F ISZ 5.39568
10 4FC7 COA 5.77617
11 4FC7 NAP 5.77617
12 2JAJ D20 5.88235
13 3FXU TSU 6.68605
14 2HJ4 PNZ 6.97674
15 2WDQ TEO 7.82609
16 1WHT BZS 8.20312
17 4XZ3 ACP 8.69565
18 4MO4 ACP 9.30233
19 1D4D SIN 10.7558
20 1XXR MAN 19.8758
Pocket No.: 4; Query (leader) PDB : 3VC3; Ligand: C6P; Similar sites found with APoc: 12
This union binding pocket(no: 4) in the query (biounit: 3vc3.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 1U1W 3HA 1.34228
2 2Y65 ADP 2.90698
3 4ZM4 PLP 3.19767
4 1L5Y BEF 3.22581
5 4G6I RS3 3.33333
6 1TUU ADP 3.48837
7 2HXW FLC 3.79747
8 5VJE GOS 4.06977
9 1GPM CIT 4.36047
10 5JBX COA 7.66284
11 2GN3 MAN 9.52381
12 5K9B FMN 17.2222
Pocket No.: 5; Query (leader) PDB : 3VC3; Ligand: C6P; Similar sites found with APoc: 4
This union binding pocket(no: 5) in the query (biounit: 3vc3.bio2) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 2O66 FLC 4.44444
2 5YRF GLC GLC 5.6338
3 3RGG AIR 5.66038
4 2H88 TEO 15.0794
Pocket No.: 6; Query (leader) PDB : 3VC3; Ligand: C6P; Similar sites found with APoc: 8
This union binding pocket(no: 6) in the query (biounit: 3vc3.bio2) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 1GJW GLC 2.90698
2 5D2H AKG 3.53357
3 4G19 GSH 3.77907
4 2DTJ THR 5.05618
5 2VZ6 FEF 5.11182
6 6B9P D0J 5.52326
7 5N9Z CAP 7.91367
8 1YNS HPO 10.7558
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