Receptor
PDB id Resolution Class Description Source Keywords
1YFS 2.08 Å EC: 6.1.1.7 THE CRYSTAL STRUCTURE OF ALANYL-TRNA SYNTHETASE IN COMPLEX WITH L-ALANINE AQUIFEX AEOLICUS ALPHA-BETA FOLD HELIX-LOOP-HELIX MOTIF AMINO ACID BINDINGLIGASE
Ref.: BREAKING SIEVE FOR STERIC EXCLUSION OF A NONCOGNATE AMINO ACID FROM ACTIVE SITE OF A TRNA SYNTHETASE. PROC.NATL.ACAD.SCI.USA V. 102 988 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ALA A:1500;
B:2500;
Valid;
Valid;
none;
none;
submit data
89.093 C3 H7 N O2 C[C@@...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1YFS 2.08 Å EC: 6.1.1.7 THE CRYSTAL STRUCTURE OF ALANYL-TRNA SYNTHETASE IN COMPLEX WITH L-ALANINE AQUIFEX AEOLICUS ALPHA-BETA FOLD HELIX-LOOP-HELIX MOTIF AMINO ACID BINDINGLIGASE
Ref.: BREAKING SIEVE FOR STERIC EXCLUSION OF A NONCOGNATE AMINO ACID FROM ACTIVE SITE OF A TRNA SYNTHETASE. PROC.NATL.ACAD.SCI.USA V. 102 988 2005
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1YFS - ALA C3 H7 N O2 C[C@@H](C(....
2 1YGB - SER C3 H7 N O3 C([C@@H](C....
3 1YFT - GLY C2 H5 N O2 C(C(=O)O)N
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1YFS - ALA C3 H7 N O2 C[C@@H](C(....
2 1YGB - SER C3 H7 N O3 C([C@@H](C....
3 1YFT - GLY C2 H5 N O2 C(C(=O)O)N
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3HXX - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
2 3HXU - A5A C13 H19 N7 O7 S C[C@@H](C(....
3 3HXW - SSA C13 H19 N7 O8 S c1nc(c2c(n....
4 3HXZ - A5A C13 H19 N7 O7 S C[C@@H](C(....
5 3HXV - G5A C12 H17 N7 O7 S c1nc(c2c(n....
6 3HXY - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
7 3HY0 - G5A C12 H17 N7 O7 S c1nc(c2c(n....
8 1YFS - ALA C3 H7 N O2 C[C@@H](C(....
9 1YGB - SER C3 H7 N O3 C([C@@H](C....
10 1YFT - GLY C2 H5 N O2 C(C(=O)O)N
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ALA; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA 1 1
2 DAL 1 1
3 VAL 0.611111 0.882353
4 THR 0.578947 0.789474
5 HGY 0.5625 0.666667
6 ABA 0.526316 0.75
7 DBB 0.526316 0.75
8 LEU 0.5 0.681818
9 ILE 0.5 0.714286
10 VAH 0.434783 0.6
11 NVA 0.434783 0.652174
12 C2N 0.428571 0.636364
13 DCY 0.428571 0.608696
14 CYS 0.428571 0.608696
15 FLA 0.428571 0.636364
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1YFS; Ligand: ALA; Similar sites found: 106
This union binding pocket(no: 1) in the query (biounit: 1yfs.bio2) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VJJ RAM GLC GAL NAG NAG GLC 0.0416 0.40384 1.50538
2 4IPH 1FJ 0.02023 0.41225 1.62602
3 4B0T ADP 0.002409 0.47396 1.72043
4 3E9I XAH 0.01672 0.40883 1.72043
5 3UH0 TSB 0.009418 0.40986 1.73913
6 4UP3 FAD 0.03214 0.40775 1.91083
7 5LVP ATP 0.02003 0.40244 1.92926
8 4MV1 ADP 0.0308 0.41193 1.93548
9 5T8U LPA 0.01695 0.40449 1.94444
10 5UGH 8AJ 0.00356 0.45096 2.01511
11 3JSX FAD 0.04022 0.40203 2.1978
12 1WNG SAH 0.02846 0.40811 2.26415
13 1X54 4AD 0.01002 0.41145 2.30415
14 4BMX ADE 0.01848 0.40167 2.39044
15 5C5H 4YB 0.0279 0.41313 2.42826
16 3KN5 ANP 0.01184 0.40829 2.46154
17 3OZV FAD 0.04531 0.41197 2.48139
18 3OZV ECN 0.04989 0.40556 2.48139
19 5UR1 YY9 0.02532 0.41592 2.57235
20 5BW4 SAM 0.01671 0.40426 2.62172
21 4YZN 4K5 0.01696 0.4078 2.78746
22 2BJK NAD 0.01598 0.43756 2.7957
23 5VAD PRO 0.00003684 0.41716 2.7957
24 5IUY BOG 0.03049 0.40473 2.86976
25 5E1M SAH 0.03396 0.40469 2.90456
26 5E1M PRO PRO LYS ARG ILE ALA 0.03396 0.40469 2.90456
27 5MW4 5JU 0.0191 0.43965 2.99401
28 3IES M24 0.01984 0.42441 3.01075
29 1NHX PEP 0.03566 0.41451 3.01075
30 1NHX FTB 0.03679 0.41451 3.01075
31 3OV6 MK0 0.01415 0.42343 3.02267
32 2EV9 SKM 0.0115 0.44236 3.04183
33 2EV9 NAP 0.0115 0.44236 3.04183
34 4I53 1C1 0.01005 0.42265 3.07263
35 2DQU CPD 0.02588 0.40103 3.19635
36 3MTX PGT 0.01327 0.42415 3.31126
37 1T90 NAD 0.02261 0.42163 3.44086
38 9LDT NAD 0.03303 0.40514 3.61446
39 4Q4K FMN 0.02594 0.4114 3.64146
40 3T1A 5MA 0.0131 0.41972 3.65591
41 3B96 MYA 0.03234 0.40944 3.65591
42 5AXH GLC GLC GLC GLC 0.0244 0.40919 3.65591
43 5KJW 53C 0.01296 0.40157 3.65591
44 5LUN ARG 0.01925 0.42419 3.69318
45 5LUN OGA 0.008591 0.42419 3.69318
46 5UIU 8CG 0.01761 0.43577 3.71517
47 5IFK HPA 0.004386 0.42397 3.84615
48 3DLG GWE 0.04052 0.42728 3.86364
49 2RCU BUJ 0.03554 0.42816 3.87097
50 4WUJ FMN 0.003926 0.44179 4.08163
51 2WPF WPF 0.02576 0.45715 4.08602
52 2WPF FAD 0.03564 0.44504 4.08602
53 4XMF HSM 0.003939 0.42695 4.34783
54 5A6N U7E 0.009775 0.41905 4.59364
55 1QY1 PRZ 0.002888 0.46373 4.5977
56 1KGI T4A 0.01291 0.42901 4.72441
57 5KF6 NAD 0.03167 0.41194 4.73118
58 4K55 H6P 0.005236 0.41667 4.83871
59 5XDT ZI7 0.02759 0.40303 4.87013
60 5E5U 1PS 0.009925 0.42401 5.02513
61 3CBC DBS 0.004873 0.40517 5.05051
62 1Y7P RIP 0.0001058 0.49647 5.38117
63 1GQG DCD 0.008968 0.42035 5.42857
64 1FDJ 2FP 0.01209 0.40821 5.50964
65 2G36 TRP 0.01333 0.40122 5.58824
66 3FW4 CAQ 0.01494 0.42174 5.61798
67 3A5Y KAA 0.001693 0.45615 5.7971
68 1CZI PRO PHI SMC NOR 0.02219 0.40952 5.88235
69 2CJ9 SSA 0.00007053 0.52697 6.02151
70 1WLE SRP 0.0008102 0.47777 6.02151
71 4EU7 CIT 0.008986 0.44102 6.02151
72 4EU7 COA 0.009334 0.43952 6.02151
73 5ML3 DL3 0.04805 0.40338 6.04027
74 5DKK FMN 0.02093 0.4008 6.2069
75 1P6O HPY 0.007784 0.41977 6.21118
76 3UDZ ADP 0.003707 0.4584 6.23656
77 2HW1 ANP 0.03685 0.41305 6.37584
78 4YNM SAM 0.01139 0.41595 6.63717
79 4X6F 3XU 0.006781 0.46277 6.66667
80 2GJ5 VD3 0.04578 0.40046 6.79012
81 5C9J STE 0.02722 0.40081 7.07071
82 4H2V AMP 0.0008856 0.46909 7.27273
83 5EYP LOC 0.0258 0.4069 7.31183
84 5LPB ADP 0.01053 0.40609 7.43243
85 4HWT 1B2 0.003788 0.43521 7.50605
86 5A89 FMN 0.03733 0.41071 7.69231
87 5A89 ADP 0.03733 0.41071 7.69231
88 1VPV PLM 0.02801 0.40239 8.66667
89 1NVT NAP 0.01401 0.42256 8.7108
90 1KBJ FMN 0.01182 0.42338 8.73786
91 2G30 ALA ALA PHE 0.001325 0.4675 8.91473
92 5XLY C2E 0.02213 0.41005 9.02256
93 5KXQ GDP 0.008094 0.42951 9.32203
94 1CBF SAH 0.0174 0.40965 10.1754
95 4M69 ANP 0.02855 0.40185 10.2473
96 5W4W 9WG 0.01972 0.40936 10.8761
97 5LJB RTL 0.01677 0.41418 12.5926
98 1QKQ MAN 0.002382 0.4226 12.6761
99 5AHW CMP 0.01753 0.40262 13.6054
100 3JRS A8S 0.01138 0.41742 14.4231
101 5HWV MBN 0.01438 0.40123 14.6154
102 5KY3 GFB 0.01442 0.43047 15
103 5W10 CMP 0.0007516 0.48513 16.4103
104 5KY4 GDP 0.007532 0.42875 17.5
105 3ZY6 GFB 0.01336 0.43032 23.2044
106 5KY9 GDP 0.009988 0.42606 25
Pocket No.: 2; Query (leader) PDB : 1YFS; Ligand: ALA; Similar sites found: 13
This union binding pocket(no: 2) in the query (biounit: 1yfs.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5J60 FAD 0.04456 0.40774 2.1875
2 5FAL SKT 0.0271 0.42569 2.45536
3 5FAL COA 0.0271 0.42569 2.45536
4 2E0N SAH 0.007348 0.43203 2.7027
5 5LXC 7AA 0.02173 0.40276 3.67647
6 4WB6 ATP 0.003761 0.46663 3.71429
7 5JZJ AN2 0.01748 0.40185 4.0404
8 1QXW M1C 0.02081 0.4118 4.7619
9 4JR7 GNP 0.01219 0.40209 5.61497
10 5U5G NAP 0.01968 0.41133 9.49153
11 5IXH OTP 0.0149 0.4443 11.8012
12 3KRU FMN 0.033 0.40455 12.828
13 5UKL SIX 0.02028 0.40436 14.5161
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