Receptor
PDB id Resolution Class Description Source Keywords
1Q8A 1.7 Å EC: 2.1.1.13 COBALAMIN-DEPENDENT METHIONINE SYNTHASE (1-566) FROM THERMOTOGA MARITIMA (CD2+:L-HCY COMPLEX, SE-MET) THERMOTOGA MARITIMA HOMOCYSTEINE METHIONINE FOLATE COBALAMIN VITAMIN B12 TRANSFERASE
Ref.: STRUCTURES OF THE N-TERMINAL MODULES IMPLY LARGE DOMAIN MOTIONS DURING CATALYSIS BY METHIONINE SYNTHASE. PROC.NATL.ACAD.SCI.USA V. 101 3729 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CD A:601;
B:602;
Invalid;
Invalid;
none;
none;
submit data
112.411 Cd [Cd+2...
HCS A:701;
B:702;
Valid;
Valid;
none;
none;
submit data
135.185 C4 H9 N O2 S C(CS)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1Q8A 1.7 Å EC: 2.1.1.13 COBALAMIN-DEPENDENT METHIONINE SYNTHASE (1-566) FROM THERMOTOGA MARITIMA (CD2+:L-HCY COMPLEX, SE-MET) THERMOTOGA MARITIMA HOMOCYSTEINE METHIONINE FOLATE COBALAMIN VITAMIN B12 TRANSFERASE
Ref.: STRUCTURES OF THE N-TERMINAL MODULES IMPLY LARGE DOMAIN MOTIONS DURING CATALYSIS BY METHIONINE SYNTHASE. PROC.NATL.ACAD.SCI.USA V. 101 3729 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1Q8A - HCS C4 H9 N O2 S C(CS)[C@@H....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1Q8A - HCS C4 H9 N O2 S C(CS)[C@@H....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1Q8A - HCS C4 H9 N O2 S C(CS)[C@@H....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: HCS; Similar ligands found: 45
No: Ligand ECFP6 Tc MDL keys Tc
1 HCS 1 1
2 CYS 0.608696 0.916667
3 DCY 0.608696 0.916667
4 DAB 0.56 0.851852
5 HSE 0.56 0.821429
6 GGL 0.555556 0.714286
7 GLU 0.555556 0.714286
8 DGL 0.555556 0.714286
9 NVA 0.538462 0.740741
10 API 0.538462 0.689655
11 DBB 0.5 0.692308
12 DSN 0.5 0.777778
13 DGN 0.5 0.645161
14 2RA 0.5 0.75
15 SER 0.5 0.777778
16 ABA 0.5 0.692308
17 GLN 0.5 0.645161
18 ORN 0.482759 0.814815
19 C2N 0.48 0.730769
20 ONL 0.466667 0.645161
21 NLE 0.466667 0.689655
22 CSS 0.464286 0.75
23 ASP 0.461538 0.655172
24 DAS 0.461538 0.655172
25 MET 0.451613 0.733333
26 MED 0.451613 0.733333
27 MSE 0.451613 0.65625
28 DLY 0.451613 0.785714
29 UN1 0.451613 0.689655
30 11C 0.451613 0.689655
31 DHH 0.4375 0.666667
32 LYS 0.4375 0.758621
33 KKA 0.428571 0.685714
34 LEU 0.428571 0.642857
35 CSO 0.428571 0.636364
36 AS2 0.428571 0.642857
37 NPI 0.424242 0.666667
38 ONH 0.424242 0.611111
39 6CL 0.411765 0.666667
40 26P 0.411765 0.625
41 2FM 0.411765 0.758621
42 3GC 0.410256 0.705882
43 VUR 0.410256 0.657143
44 CIR 0.4 0.611111
45 MF3 0.4 0.733333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1Q8A; Ligand: HCS; Similar sites found: 121
This union binding pocket(no: 1) in the query (biounit: 1q8a.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3C0G 3AM 0.0259 0.40375 1.7094
2 1XC6 GAL 0.008201 0.41658 1.76678
3 2V58 LZJ 0.03893 0.41638 1.78174
4 5JY4 ISC 0.005846 0.43222 1.79028
5 1GQ2 NAP 0.01538 0.42482 1.8018
6 3EWC MCF 0.02147 0.4134 1.88679
7 4XQC 13D 0.03359 0.42243 1.89474
8 1CM8 ANP 0.02071 0.40083 1.90736
9 5VCV 1N1 0.02611 0.40559 1.92926
10 5HSA FAS 0.02919 0.4231 1.94346
11 5KGS 6SR 0.03345 0.4222 1.96937
12 3TWO NDP 0.03234 0.41421 2.01149
13 2WL5 COA 0.02524 0.40633 2.04082
14 2WKT COA 0.0247 0.4036 2.04082
15 3DJF BC3 0.01803 0.41566 2.09059
16 2WU6 DKI 0.002962 0.45436 2.09974
17 4A2A ATP 0.01034 0.42512 2.14797
18 4CQE CQE 0.02581 0.40443 2.15827
19 4MS4 2C0 0.02396 0.4001 2.29682
20 5U7D 19F 0.04137 0.4026 2.31884
21 2SFP PPI 0.01798 0.40689 2.31959
22 4LUT DCS 0.01976 0.40639 2.33766
23 1UNH IXM 0.01382 0.40722 2.40385
24 5H81 NAP 0.02334 0.40796 2.57069
25 2VQD AP2 0.01584 0.41369 2.58621
26 4GKV NAD 0.04089 0.4075 2.67857
27 4E1O PLP PVH 0.009188 0.42902 2.7027
28 2Q7V FAD 0.04623 0.41258 2.76923
29 3NZK C90 0.02346 0.40302 2.89389
30 5LXC 7AA 0.009601 0.41715 2.94118
31 4BCM T7Z 0.01084 0.40615 2.99003
32 5W10 CMP 0.02487 0.40168 3.07692
33 1R37 NAD 0.009043 0.44358 3.17003
34 4CSV STI 0.008418 0.43168 3.27273
35 1KYZ FER 0.04404 0.40016 3.28767
36 4XB4 45D 0.02247 0.40969 3.28947
37 5MY8 RXZ 0.02367 0.40971 3.39426
38 5ETJ IM5 0.03983 0.41111 3.39506
39 5FAG PPI 0.003383 0.44606 3.41463
40 4QTB 38Z 0.01191 0.43185 3.42105
41 4W6Z 8ID 0.04627 0.40675 3.45821
42 1KOL NAD 0.03294 0.41633 3.51759
43 1YY5 FAD 0.02855 0.42602 3.7037
44 1V7C HEY 0.0196 0.41928 3.7037
45 1KEV NDP 0.04961 0.40428 3.7037
46 1MRH FMC 0.01362 0.40137 3.80228
47 3BY9 SIN 0.003972 0.42374 3.84615
48 1NFQ NAI 0.0405 0.40633 3.84615
49 2IO8 ADP 0.01768 0.41619 3.88693
50 3E7O 35F 0.03753 0.40722 3.88889
51 4ZUL UN1 0.02533 0.41585 3.89864
52 3BQD DAY 0.02896 0.40117 3.92157
53 2GCG DGY 0.00189 0.40321 3.93939
54 2WEL K88 0.00197 0.43844 4
55 5ECP ATP 0.04598 0.4124 4.03587
56 4L2I FAD 0.04311 0.40978 4.04624
57 4IZY 1J2 0.01181 0.42137 4.06504
58 1LLU NAD 0.01717 0.42964 4.09357
59 5H2U 1N1 0.01034 0.41601 4.11985
60 1M2T ADE 0.01549 0.40384 4.18251
61 5JFS 6K0 0.01549 0.43683 4.22078
62 2RJH DCS 0.02034 0.40236 4.22164
63 1PN0 IPH 0.03929 0.42196 4.24028
64 1PN0 FAD 0.03935 0.42182 4.24028
65 2BEK ATP 0.03032 0.40117 4.28016
66 5O4J PJL 0.04336 0.40551 4.37956
67 3WLE NAD 0.00644 0.45484 4.39883
68 2VPQ ANP 0.01951 0.4123 4.43459
69 2HK5 1BM 0.02158 0.40726 4.44444
70 2A8Y MTA 0.0273 0.40162 4.44444
71 3MDV CL6 0.04038 0.40801 4.60526
72 4A4X JUP 0.02546 0.40977 4.6595
73 4JR7 GNP 0.02317 0.40169 4.81283
74 1PK8 ATP 0.008592 0.43516 4.9763
75 3ZEI AWH 0.04057 0.40306 5.16129
76 5L2Z 70C 0.02966 0.4165 5.17241
77 4NBU NAI 0.04528 0.40305 5.2
78 4KCT PYR 0.01358 0.40248 5.21042
79 3O61 GDD 0.01325 0.42235 5.2356
80 5B4B LP5 0.03572 0.40676 5.24194
81 2ZYJ PGU 0.02104 0.41493 5.28967
82 5VZ0 ADP 0.009955 0.41918 5.30035
83 3ZRM ZRM 0.01198 0.41579 5.39084
84 1I7L ATP 0.009157 0.43178 5.50162
85 3QKT ANP 0.02492 0.40933 5.60472
86 3C1X CKK 0.02105 0.40885 5.89812
87 5X8I SQZ 0.02179 0.40188 6.35838
88 1XG5 NAP 0.03159 0.41034 6.45161
89 4CQM NAP 0.02718 0.4145 6.51341
90 3O5X JZG 0.00263 0.44533 6.52174
91 1RP0 AHZ 0.04111 0.40579 6.69014
92 5KO1 6UY 0.004372 0.43744 7.06714
93 1AUX AGS 0.01379 0.41381 7.07396
94 5TIV A3P 0.03755 0.41753 7.11462
95 3B8X G4M 0.04961 0.4031 7.17949
96 4LOO SB4 0.02077 0.40311 7.47922
97 5EPO NAP 0.02782 0.41394 7.63359
98 4F9C 0SX 0.01923 0.4041 7.63889
99 3KMW ATP 0.01942 0.40308 7.75194
100 2OO8 RAJ 0.006982 0.43443 7.88644
101 4XBA 5GP 0.02027 0.40055 8
102 5GUD 2IT 0.03676 0.41382 8.06794
103 2B9H ADP 0.02544 0.40057 8.2153
104 5EYP LOC 0.01496 0.41888 8.28402
105 3D5Z FUB AHR AHR 0.01587 0.41296 8.9172
106 3KPB SAM 0.002439 0.45311 9.01639
107 2WSB NAD 0.03616 0.41746 9.44882
108 5VC5 96M 0.03586 0.40324 12.4567
109 4BKJ STI 0.01531 0.42053 12.6984
110 1F2U ATP 0.03502 0.4034 12.7517
111 1EYQ NAR 0.01355 0.40348 13.0631
112 1E3W NAD 0.03612 0.40775 14.5594
113 1CDO NAD 0.03091 0.40679 14.9733
114 3LGS SAH 0.01851 0.4091 15.3558
115 3LGS ADE 0.01851 0.4091 15.3558
116 3D78 NBB 0.021 0.4121 15.9664
117 4H4D 10E 0.01564 0.4042 17.3375
118 1E7S NAP 0.04994 0.40278 18.0685
119 3TYZ PAB 0.02329 0.41275 27.8571
120 4M3P HCS 0.00000005626 0.69999 31.5271
121 5DMM HCS 0.0000004754 0.57165 41.2903
Pocket No.: 2; Query (leader) PDB : 1Q8A; Ligand: HCS; Similar sites found: 42
This union binding pocket(no: 2) in the query (biounit: 1q8a.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5A1S FLC 0.007798 0.4091 1.33929
2 1K7L 544 0.03985 0.40065 1.38889
3 5M7S NHT 0.02051 0.40657 1.59011
4 1JS3 PLP 142 0.0112 0.42099 1.64609
5 5JXZ ISC 0.005804 0.43449 1.79028
6 3O26 NDP 0.02607 0.41483 1.92926
7 2Q2V NAD 0.04375 0.40527 1.96078
8 1ZAP A70 0.03996 0.40285 2.04678
9 2DKH 3HB 0.02034 0.43142 2.12014
10 4LGY ADP 0.02601 0.40327 2.12014
11 2Q2A ARG 0.006893 0.42304 2.20588
12 1PJS SAH 0.02864 0.40044 2.407
13 5JWI ARG GLU 0.02467 0.40051 2.4735
14 1GSA ADP 0.02463 0.40705 2.53165
15 3ZS9 ADP ALF 0.02974 0.40719 2.54237
16 1QFY NAP 0.04305 0.41094 2.5974
17 1QFY FAD 0.04305 0.41094 2.5974
18 4PNE SAH 0.007631 0.43685 2.98013
19 3VHE 42Q 0.04503 0.40018 3.06407
20 5TO8 7FM 0.0141 0.43676 3.5461
21 4IDC 1XX 0.04053 0.40891 3.61446
22 4IDC NDP 0.04053 0.40891 3.61446
23 5U23 TQP 0.04612 0.40331 3.66492
24 1SMR PIV HIS PRO PHE HIS LPL TYR TYR SER 0.04802 0.40439 3.8806
25 4XGU ADP 0.02196 0.40439 4.00943
26 1D6S MET PLP 0.01241 0.42511 4.03727
27 4L2I NAD 0.03604 0.42162 4.04624
28 2I6A 5I5 0.02559 0.4009 4.34783
29 3LN0 52B 0.04258 0.41935 4.41696
30 5MJA 7O3 0.008927 0.41951 4.59016
31 4MO2 FDA 0.04446 0.41017 5.43478
32 4U0I 0LI 0.02027 0.42083 5.71429
33 4YAG NAI 0.03118 0.42293 6.57439
34 3SJ7 NDP 0.04112 0.40251 6.74603
35 2XCM ADP 0.01732 0.40506 7.00935
36 4YZC STU 0.04547 0.40653 7.40741
37 5W4W 9WG 0.04068 0.40254 7.55287
38 5GUD NDP 0.04115 0.41293 8.06794
39 5GUD CIT 0.04429 0.40871 8.06794
40 1I0Z NAI 0.0258 0.41423 8.10811
41 1WP4 NDP 0.03054 0.40836 10.0346
42 3TYZ XHP 0.01631 0.41862 27.8571
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