Receptor
PDB id Resolution Class Description Source Keywords
2YIM 1.41 Å EC: 5.1.99.4 THE ENOLISATION CHEMISTRY OF A THIOESTER-DEPENDENT RACEMASE: THE 1.4 A CRYSTAL STRUCTURE OF A COMPLEX WITH A P LANAR REACTION INTERMEDIATE ANALOGUE MYCOBACTERIUM TUBERCULOSIS ISOMERASE METHYL-COA RACEMASE TRANSITION STATE MOLECULAR DYNAMICS QM/MM OXYANION HOLE
Ref.: THE ENOLIZATION CHEMISTRY OF A THIOESTER-DEPENDENT RACEMASE: THE 1.4 A CRYSTAL STRUCTURE OF A REACTION INTERMEDIATE COMPLEX CHARACTERIZED BY DETAILED QM/M CALCULATIONS. J PHYS CHEM B V. 116 3619 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1361;
B:1362;
C:1361;
C:1362;
D:1362;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MC4 A:1363;
B:1363;
C:1363;
D:1363;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 120 uM
864.626 C26 H41 N7 O18 P3 S C/C(=...
PO4 B:1361;
D:1361;
Invalid;
Invalid;
none;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2GCE 1.85 Å EC: 5.1.99.4 THE 1,1-PROTON TRANSFER REACTION MECHANISM BY ALPHA- METHYLACYL-COA RACEMASE IS CATALYZED BY AN A SPARTATE/HISTIDINE PAIR AND INVOLVES A SMOOTH, METHIONINE-RI CH SURFACE FOR BINDING THE FATTY ACYL MOIETY MYCOBACTERIUM TUBERCULOSIS ALPHA-METHYLACYL-COA RACEMASE RACEMASE COA TRANSFERASE PROTON TRANSFER COENZYME A ISOMERASE
Ref.: THE CATALYSIS OF THE 1,1-PROTON TRANSFER BY ALPHA-METHYL-ACYL-COA RACEMASE IS COUPLED TO A MOVEMENT OF THE FATTY ACYL MOIETY OVER A HYDROPHOBIC, METHIONINE-RICH SURFACE J.MOL.BIOL. V. 367 1145 2007
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2YIM Kd = 120 uM MC4 C26 H41 N7 O18 P3 S C/C(=C([O-....
2 2GD6 - ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
3 2GCI - MRR C36 H64 N7 O17 P3 S CCCCCCCCCC....
4 2GD0 - MRS C36 H64 N7 O17 P3 S CCCCCCCCCC....
5 2GD2 - CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
6 2GCE Kd = 24.5 uM RFC C34 H53 N7 O17 P3 S CC(C)Cc1cc....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2YIM Kd = 120 uM MC4 C26 H41 N7 O18 P3 S C/C(=C([O-....
2 2GD6 - ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
3 2GCI - MRR C36 H64 N7 O17 P3 S CCCCCCCCCC....
4 2GD0 - MRS C36 H64 N7 O17 P3 S CCCCCCCCCC....
5 2GD2 - CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
6 2GCE Kd = 24.5 uM RFC C34 H53 N7 O17 P3 S CC(C)Cc1cc....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2YIM Kd = 120 uM MC4 C26 H41 N7 O18 P3 S C/C(=C([O-....
2 2GD6 - ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
3 2GCI - MRR C36 H64 N7 O17 P3 S CCCCCCCCCC....
4 2GD0 - MRS C36 H64 N7 O17 P3 S CCCCCCCCCC....
5 2GD2 - CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
6 2GCE Kd = 24.5 uM RFC C34 H53 N7 O17 P3 S CC(C)Cc1cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MC4; Similar ligands found: 134
No: Ligand ECFP6 Tc MDL keys Tc
1 MC4 1 1
2 ACO 0.887097 0.935484
3 3KK 0.84375 0.945652
4 CAO 0.84127 0.894737
5 COS 0.84127 0.904255
6 2MC 0.838462 0.967742
7 OXK 0.837209 0.924731
8 SOP 0.837209 0.924731
9 1VU 0.830769 0.935484
10 CO6 0.830769 0.945652
11 CAA 0.825758 0.934783
12 COK 0.823077 0.904255
13 1HE 0.818182 0.905263
14 BCO 0.818182 0.924731
15 IVC 0.818182 0.934783
16 MLC 0.818182 0.924731
17 3HC 0.818182 0.934783
18 CMC 0.816794 0.904255
19 FYN 0.815385 0.923913
20 30N 0.8125 0.85
21 MCA 0.81203 0.935484
22 COO 0.81203 0.945652
23 SCA 0.80597 0.924731
24 0T1 0.80315 0.903226
25 COA 0.80315 0.923913
26 DCA 0.801587 0.903226
27 HXC 0.801471 0.925532
28 HGG 0.8 0.924731
29 1GZ 0.8 0.935484
30 COW 0.8 0.914894
31 BYC 0.8 0.924731
32 IRC 0.8 0.934783
33 FAQ 0.794118 0.924731
34 BCA 0.794118 0.914894
35 A1S 0.791045 0.904255
36 2NE 0.789855 0.905263
37 GRA 0.788321 0.924731
38 ETB 0.787402 0.87234
39 COF 0.786765 0.885417
40 AMX 0.784615 0.913043
41 TGC 0.782609 0.914894
42 2CP 0.779412 0.914894
43 SCO 0.778626 0.903226
44 CMX 0.778626 0.903226
45 CO8 0.776978 0.925532
46 1CZ 0.776978 0.914894
47 2KQ 0.773723 0.925532
48 3CP 0.773723 0.904255
49 CS8 0.77305 0.915789
50 FAM 0.772727 0.884211
51 FCX 0.772727 0.875
52 MYA 0.771429 0.925532
53 ST9 0.771429 0.925532
54 UCC 0.771429 0.925532
55 DCC 0.771429 0.925532
56 MFK 0.771429 0.925532
57 5F9 0.771429 0.925532
58 SCD 0.77037 0.903226
59 4CA 0.768116 0.894737
60 HAX 0.766917 0.884211
61 NMX 0.762963 0.858586
62 WCA 0.760563 0.925532
63 0FQ 0.758865 0.904255
64 4CO 0.758865 0.894737
65 MCD 0.755556 0.904255
66 CA6 0.755556 0.843137
67 4KX 0.755245 0.956989
68 UOQ 0.755245 0.905263
69 NHM 0.755245 0.905263
70 NHW 0.755245 0.905263
71 HDC 0.755245 0.925532
72 01A 0.753521 0.867347
73 CIC 0.751773 0.904255
74 HFQ 0.75 0.885417
75 MRS 0.75 0.925532
76 MRR 0.75 0.925532
77 YNC 0.744828 0.935484
78 DAK 0.744828 0.915789
79 CAJ 0.744526 0.904255
80 0ET 0.741259 0.905263
81 8Z2 0.739726 0.93617
82 1CV 0.736111 0.924731
83 YE1 0.733813 0.893617
84 1HA 0.731544 0.905263
85 01K 0.726667 0.924731
86 CA8 0.723404 0.843137
87 NHQ 0.718121 0.913979
88 CCQ 0.715278 0.926316
89 COT 0.710526 0.904255
90 S0N 0.703448 0.884211
91 CA3 0.690323 0.904255
92 CA5 0.679245 0.867347
93 UCA 0.675 0.925532
94 CO7 0.673611 0.945652
95 93P 0.664596 0.894737
96 93M 0.654545 0.894737
97 COD 0.651852 0.913043
98 5TW 0.626437 0.947368
99 4BN 0.626437 0.947368
100 OXT 0.614943 0.907216
101 HMG 0.614379 0.913979
102 COA MYR 0.596154 0.914894
103 PLM COA 0.596154 0.914894
104 COA PLM 0.596154 0.914894
105 JBT 0.582418 0.87
106 BSJ 0.567416 0.876289
107 PAP 0.552846 0.75
108 ACE SER ASP ALY THR NH2 COA 0.515957 0.904255
109 191 0.50625 0.918367
110 SFC 0.505952 0.946237
111 RFC 0.505952 0.946237
112 PPS 0.503876 0.7
113 A3P 0.491935 0.73913
114 0WD 0.486667 0.787234
115 PTJ 0.43662 0.806452
116 3AM 0.432 0.728261
117 PAJ 0.428571 0.817204
118 3OD 0.426573 0.763441
119 ATR 0.425373 0.73913
120 PUA 0.425 0.778947
121 A22 0.42446 0.752688
122 ADP 0.419847 0.76087
123 A2D 0.418605 0.741935
124 AGS 0.414815 0.765957
125 SAP 0.414815 0.765957
126 OAD 0.412587 0.763441
127 48N 0.407895 0.768421
128 2A5 0.407407 0.782609
129 A2R 0.407143 0.752688
130 A A A 0.402778 0.771739
131 NA7 0.402778 0.793478
132 BA3 0.401515 0.741935
133 YLB 0.4 0.840426
134 ATP 0.4 0.76087
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2GCE; Ligand: SFC; Similar sites found: 21
This union binding pocket(no: 1) in the query (biounit: 2gce.bio2) has 43 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2Q3M MLA 0.03921 0.41662 1.22699
2 2QES ADE 0.03455 0.41769 2.68199
3 5TCI MLI 0.03608 0.40837 3.26087
4 5FUS DAO 0.04265 0.40329 3.83275
5 2F5X ASP 0.04047 0.41531 3.84615
6 3GFS FMN 0.03004 0.41122 4.5977
7 3UVD MB3 0.04907 0.40703 4.83871
8 3RKR NAP 0.03273 0.41277 5.34351
9 1YXM ADE 0.01334 0.44137 6.27063
10 3KO0 TFP 0.01224 0.44703 6.93069
11 5UGW GSH 0.04352 0.40185 7.42857
12 2UYQ SAM 0.03501 0.41647 8.70968
13 2P8O BVA 0.01611 0.41487 12.2137
14 1DKU AP2 0.02217 0.42956 12.6183
15 5XNA SHV 0.02498 0.42511 13.0435
16 1Q7E MET 0.00002041 0.42072 27.5
17 1VGR COA 0.0000003559 0.48815 28.3333
18 2VJM COA 0.00000006968 0.48349 28.6111
19 3UBM COA 0.0000007644 0.44794 34.8684
20 1XVV CCQ 0.0002091 0.43613 39.1667
21 5E8J SAH 0.04272 0.40009 40.9091
Pocket No.: 2; Query (leader) PDB : 2GCE; Ligand: RFC; Similar sites found: 14
This union binding pocket(no: 2) in the query (biounit: 2gce.bio2) has 43 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1HPG BOC ALA ALA PRO GLU 0.04211 0.40358 3.20856
2 1O9P MLA 0.04981 0.40651 4.16667
3 3W9F I3P 0.03282 0.44073 4.61538
4 1KQR MNA 0.04959 0.40126 5.58659
5 1CEB AMH 0.03272 0.42202 5.68182
6 4G86 BNT 0.03644 0.43159 5.98592
7 1YXM ADE 0.02533 0.41999 6.27063
8 4V0K GDP 0.02785 0.40046 7.10059
9 1DKU AP2 0.03676 0.41055 12.6183
10 3JUT GTQ 0.02819 0.42028 26.1538
11 1VGR COA 0.0000003637 0.56109 28.3333
12 2VJM COA 0.00000007953 0.61975 28.6111
13 3UBM COA 0.00000008837 0.47137 34.8684
14 1XA4 COA 0.0000746 0.50276 40.8333
Pocket No.: 3; Query (leader) PDB : 2GCE; Ligand: SFC; 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: 2gce.bio2) has 43 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2GCE; Ligand: RFC; 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: 2gce.bio2) has 40 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2GCE; Ligand: RFC; 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: 2gce.bio1) has 40 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2GCE; Ligand: SFC; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2gce.bio1) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2GCE; Ligand: RFC; Similar sites found: 6
This union binding pocket(no: 7) in the query (biounit: 2gce.bio1) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4RM0 FUC NDG GAL 0.04759 0.4158 3.16456
2 2AWN ADP 0.0498 0.41861 3.33333
3 3RKR NAP 0.0459 0.4041 5.34351
4 5XNA SHV 0.04581 0.40636 13.0435
5 1Q7E MET 0.00004641 0.41324 27.5
6 1XVV CCQ 0.0002258 0.43384 39.1667
Pocket No.: 8; Query (leader) PDB : 2GCE; Ligand: SFC; Similar sites found: 1
This union binding pocket(no: 8) in the query (biounit: 2gce.bio1) has 43 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1ZOY UQ1 0.04714 0.41535 8.73786
Feedback