Receptor
PDB id Resolution Class Description Source Keywords
7REQ 2.2 Å EC: 5.4.99.2 METHYLMALONYL-COA MUTASE, 2-CARBOXYPROPYL-COA INHIBITOR COMP PROPIONIBACTERIUM FREUDENREICHII SUBSPSHERMANII ISOMERASE MUTASE INTRAMOLECULAR TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF SUBSTRATE COMPLEXES OF METHYLMALONYL-COA MUTASE. BIOCHEMISTRY V. 38 7999 1999
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2CP A:1801;
C:2801;
Valid;
Valid;
none;
none;
submit data
853.623 C25 H42 N7 O18 P3 S C[C@@...
B12 A:1800;
C:2800;
Part of Protein;
Part of Protein;
none;
none;
submit data
1330.36 C62 H89 Co N13 O14 P Cc1cc...
GOL B:3001;
B:3002;
D:3003;
D:3004;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1REQ 2 Å EC: 5.4.99.2 METHYLMALONYL-COA MUTASE PROPIONIBACTERIUM FREUDENREICHII SUBSPSHERMANII ISOMERASE MUTASE INTRAMOLECULAR TRANSFERASE
Ref.: HOW COENZYME B12 RADICALS ARE GENERATED: THE CRYSTA STRUCTURE OF METHYLMALONYL-COENZYME A MUTASE AT 2 A RESOLUTION. STRUCTURE V. 4 339 1996
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 6REQ - 3CP C25 H42 N7 O18 P3 S CC(C)(CO[P....
2 2REQ - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 5REQ - MCD C26 H42 N7 O19 P3 C[C@@H](C(....
4 4REQ - MCA C25 H40 N7 O19 P3 S C[C@H](C(=....
5 7REQ - 2CP C25 H42 N7 O18 P3 S C[C@@H](CS....
6 1REQ - DCA C21 H36 N7 O16 P3 CCNC(=O)CC....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 6REQ - 3CP C25 H42 N7 O18 P3 S CC(C)(CO[P....
2 2REQ - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 5REQ - MCD C26 H42 N7 O19 P3 C[C@@H](C(....
4 4REQ - MCA C25 H40 N7 O19 P3 S C[C@H](C(=....
5 7REQ - 2CP C25 H42 N7 O18 P3 S C[C@@H](CS....
6 1REQ - DCA C21 H36 N7 O16 P3 CCNC(=O)CC....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 6REQ - 3CP C25 H42 N7 O18 P3 S CC(C)(CO[P....
2 2REQ - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 5REQ - MCD C26 H42 N7 O19 P3 C[C@@H](C(....
4 4REQ - MCA C25 H40 N7 O19 P3 S C[C@H](C(=....
5 7REQ - 2CP C25 H42 N7 O18 P3 S C[C@@H](CS....
6 1REQ - DCA C21 H36 N7 O16 P3 CCNC(=O)CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2CP; Similar ligands found: 133
No: Ligand ECFP6 Tc MDL keys Tc
1 2CP 1 1
2 CMC 0.859375 0.988636
3 SOP 0.851562 0.988636
4 A1S 0.846154 0.966292
5 ACO 0.84252 0.955556
6 COS 0.84127 0.944444
7 CAO 0.84127 0.934066
8 FYN 0.829457 0.965909
9 3CP 0.827068 0.988636
10 MCA 0.825758 0.977528
11 OXK 0.823077 0.966292
12 4CA 0.820895 0.955556
13 MLC 0.818182 0.966292
14 0ET 0.817518 0.966667
15 COA 0.81746 0.965909
16 CO6 0.816794 0.966292
17 CIC 0.816176 0.988636
18 3KK 0.815385 0.966292
19 COF 0.813433 0.945055
20 MCD 0.80916 0.966292
21 COK 0.80916 0.944444
22 SCO 0.806202 0.965909
23 IVC 0.804511 0.955056
24 3HC 0.804511 0.955056
25 0T1 0.80315 0.94382
26 1VU 0.80303 0.955556
27 DCA 0.801587 0.94382
28 FAM 0.8 0.923077
29 FCX 0.8 0.934066
30 30N 0.79845 0.885417
31 2MC 0.796992 0.924731
32 SCA 0.792593 0.966292
33 CMX 0.792308 0.965909
34 BCO 0.791045 0.944444
35 1HE 0.791045 0.945055
36 ETB 0.787402 0.911111
37 HGG 0.786765 0.966292
38 2KQ 0.786765 0.966667
39 IRC 0.786765 0.955056
40 COO 0.785185 0.944444
41 CAA 0.785185 0.955056
42 AMX 0.784615 0.954545
43 4CO 0.784173 0.955556
44 0FQ 0.784173 0.966292
45 TGC 0.782609 0.977528
46 MC4 0.779412 0.914894
47 01A 0.778571 0.924731
48 GRA 0.775362 0.966292
49 COW 0.773723 0.934066
50 1GZ 0.773723 0.934066
51 BYC 0.773723 0.944444
52 SCD 0.77037 0.965909
53 FAQ 0.768116 0.944444
54 BCA 0.768116 0.934066
55 NHW 0.767606 0.966667
56 UOQ 0.767606 0.966667
57 NHM 0.767606 0.966667
58 HAX 0.766917 0.923077
59 NHQ 0.765517 0.977273
60 1CZ 0.764286 0.955556
61 HXC 0.76259 0.945055
62 HFQ 0.762238 0.945055
63 MRS 0.762238 0.945055
64 MRR 0.762238 0.945055
65 CA6 0.755556 0.896907
66 2NE 0.751773 0.923913
67 CO8 0.751773 0.945055
68 01K 0.75 0.988636
69 NMX 0.75 0.875
70 1CV 0.748252 0.966292
71 CS8 0.748252 0.956044
72 MFK 0.746479 0.945055
73 UCC 0.746479 0.945055
74 MYA 0.746479 0.945055
75 5F9 0.746479 0.945055
76 ST9 0.746479 0.945055
77 DCC 0.746479 0.945055
78 CAJ 0.744526 0.966292
79 HDC 0.743056 0.945055
80 WCA 0.736111 0.923913
81 YE1 0.733813 0.933333
82 4KX 0.731034 0.913979
83 CA8 0.723404 0.858586
84 COT 0.721854 0.966292
85 YNC 0.721088 0.934066
86 DAK 0.721088 0.934783
87 93P 0.717949 0.977528
88 8Z2 0.716216 0.934783
89 S0N 0.715278 0.944444
90 CA3 0.712418 0.966292
91 1HA 0.697368 0.923913
92 93M 0.695652 0.977528
93 CCQ 0.691781 0.945652
94 CA5 0.689873 0.924731
95 UCA 0.664596 0.945055
96 COD 0.664179 0.954545
97 CO7 0.650685 0.944444
98 5TW 0.617143 0.905263
99 4BN 0.617143 0.905263
100 OXT 0.614943 0.905263
101 JBT 0.59116 0.90625
102 HMG 0.583333 0.933333
103 BSJ 0.576271 0.956044
104 COA PLM 0.575949 0.913043
105 PLM COA 0.575949 0.913043
106 COA MYR 0.575949 0.913043
107 PAP 0.540323 0.784091
108 ACE SER ASP ALY THR NH2 COA 0.524064 0.966292
109 RFC 0.505952 0.945055
110 SFC 0.505952 0.945055
111 PPS 0.492308 0.729167
112 A3P 0.491935 0.772727
113 191 0.487654 0.858586
114 0WD 0.476821 0.763441
115 PTJ 0.446809 0.863636
116 PUA 0.433962 0.793478
117 3AM 0.432 0.761364
118 A22 0.42446 0.786517
119 A2D 0.418605 0.775281
120 PAJ 0.41844 0.875
121 48N 0.417219 0.822222
122 3OD 0.416667 0.818182
123 AGS 0.414815 0.78022
124 SAP 0.414815 0.78022
125 ATR 0.414815 0.772727
126 ADP 0.409091 0.795455
127 A2R 0.407143 0.806818
128 TXA 0.406897 0.808989
129 NA7 0.402778 0.829545
130 OAD 0.402778 0.818182
131 BA3 0.401515 0.775281
132 YLB 0.4 0.898876
133 ATP 0.4 0.795455
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1REQ; Ligand: DCA; Similar sites found: 110
This union binding pocket(no: 1) in the query (biounit: 1req.bio2) has 43 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1SR9 KIV 0.03703 0.41767 1.72684
2 3O2K DST 0.03529 0.41864 2.1097
3 3B6R ADP 0.03195 0.4034 2.3622
4 1DJX I3P 0.01347 0.43316 2.40385
5 4AMW 5DI 0.03568 0.4178 2.51177
6 4KCT PYR 0.01732 0.43146 2.80561
7 1U6R ADP 0.01632 0.41459 2.89474
8 1G51 AMP 0.01892 0.43314 2.93103
9 2JBM SRT 0.02914 0.40757 3.01003
10 3GD9 GLC BGC BGC BGC 0.006733 0.44468 3.26975
11 2ICK DMA 0.04848 0.40038 3.43348
12 2VEG PMM 0.03284 0.41641 3.45369
13 5MRH Q9Z 0.047 0.4079 3.45369
14 4FXQ G9L 0.01952 0.4333 3.47826
15 4RW3 IPD 0.008608 0.44783 3.64238
16 3H22 B53 0.0165 0.42105 3.7037
17 2CIR BG6 0.04052 0.41531 3.7037
18 3A16 PXO 0.008536 0.43311 3.75335
19 3P7N FMN 0.0253 0.40245 3.87597
20 3U6W KIV 0.04676 0.41234 3.98126
21 2J5B TYE 0.01526 0.43315 4.02299
22 2XG5 EC2 0.01847 0.41849 4.04624
23 2XG5 EC5 0.01847 0.41849 4.04624
24 5F7J ADE 0.01797 0.43658 4.0625
25 4D4U FUC GAL 0.006684 0.45332 4.12698
26 1VJ7 GPX 0.02018 0.42679 4.3257
27 4NZF ARB 0.04657 0.41188 4.46429
28 2R5V HHH 0.02206 0.41816 4.48179
29 1EYE PMM 0.04825 0.40048 4.64286
30 4HWT 1B2 0.01606 0.41183 4.84262
31 4H6B 10Y 0.04857 0.40362 5.12821
32 4H6B 10X 0.04878 0.40023 5.12821
33 1H8S AIC 0.04661 0.4081 5.15873
34 3MI3 LYS 0.04557 0.41241 5.20095
35 5M77 7K2 7K3 0.042 0.40364 5.26316
36 1ULE GLA GAL NAG 0.03703 0.40385 5.33333
37 3PGU OLA 0.03878 0.40885 5.38642
38 2IUW AKG 0.03832 0.41275 5.46218
39 1VRP ADP 0.01355 0.42536 5.51181
40 5MX4 HPA 0.003481 0.47484 5.5794
41 2GVJ DGB 0.002616 0.44537 5.70265
42 2Y5S 78H 0.02047 0.41984 5.78231
43 4JH6 FCN 0.04625 0.40829 5.7971
44 2G30 ALA ALA PHE 0.0002545 0.47434 5.81395
45 1NKI PPF 0.02064 0.4316 5.92593
46 4J0M BLD 0.04546 0.40184 5.96546
47 1OPB RET 0.02407 0.40348 5.97015
48 3KYF 5GP 5GP 0.03853 0.409 6.06061
49 4XDA RIB 0.02224 0.42166 6.14887
50 1F52 ADP 0.03721 0.40638 6.19658
51 1MH5 HAL 0.01438 0.40031 6.84932
52 3T7V MD0 0.03923 0.41606 6.85714
53 4WOE ADP 0.002542 0.48483 6.90738
54 3CBC DBS 0.04737 0.40265 7.07071
55 3BJE URA 0.01073 0.44767 7.16332
56 1Y9Q MED 0.03979 0.41452 7.29167
57 2A5F NAD 0.04102 0.40099 7.42857
58 1AJ0 PH2 0.03421 0.40192 7.44681
59 3LGS ADE 0.02034 0.43212 7.49064
60 1EX7 5GP 0.03272 0.42047 7.52688
61 4BG4 ADP 0.01161 0.42175 7.58427
62 4LIT AKG 0.01338 0.44346 7.61671
63 4DSU BZI 0.00572 0.46377 7.93651
64 5NBW 8SK 0.03816 0.40581 8.10811
65 4IF4 BEF 0.02331 0.40545 8.17308
66 5BTX CMP 0.01321 0.44182 8.21918
67 1DZK PRZ 0.03563 0.40104 8.28025
68 4RYV ZEA 0.03323 0.41242 8.3871
69 3H0L ADP 0.001742 0.48507 8.51064
70 3THR C2F 0.0244 0.40921 8.53242
71 2Y7P SAL 0.03183 0.42114 8.7156
72 5LUN OGA 0.0355 0.41849 8.80682
73 4JN6 OXL 0.04068 0.40757 8.82353
74 2C49 ADN 0.02927 0.40229 8.9404
75 2P7Q GG6 0.03796 0.41298 9.02256
76 1KTC NGA 0.04686 0.41173 9.1358
77 2ZSC BTN 0.04211 0.40041 9.21986
78 2E27 AB0 0.03862 0.40554 10.084
79 1ZOT EMA 0.04372 0.40607 10.1449
80 3ZGJ RMN 0.01318 0.44238 10.2426
81 3SAO DBH 0.003573 0.47607 10.625
82 3SAO NKN 0.01031 0.43928 10.625
83 2VDF OCT 0.02729 0.44929 10.6719
84 1SN0 T44 0.04515 0.40199 10.7692
85 4FK7 P34 0.001397 0.48442 10.917
86 4OCT AKG 0.02671 0.41745 11.2613
87 3ZW0 FUC 0.0239 0.42758 11.4943
88 3ZW2 GAL FUC 0.02891 0.41208 11.4943
89 3ZW2 NAG GAL FUC 0.02891 0.40873 11.4943
90 1ZNY GDP 0.03085 0.42189 11.5942
91 2WZ5 MET 0.008593 0.42046 11.7647
92 3WG3 A2G GAL NAG FUC 0.02397 0.42823 11.7978
93 1Y7P RIP 0.04882 0.40792 12.5561
94 3JQ3 ADP 0.02765 0.41666 12.8415
95 2BO9 VAL 0.03465 0.41908 13.0631
96 3ESS 18N 0.03622 0.4149 13.4783
97 1P0Z FLC 0.04491 0.41302 13.7405
98 1AD4 HH2 0.01126 0.4294 14.2857
99 2YKL NLD 0.01375 0.42876 14.3519
100 5EWK P34 0.02492 0.42687 14.5
101 4B1M FRU FRU 0.01103 0.44684 15.1351
102 1IIU RTL 0.0173 0.40456 16.092
103 4COQ SAN 0.04524 0.41233 16.1943
104 4B1L FRU 0.01793 0.43023 16.9697
105 4CSD MFU 0.04248 0.41303 17.2794
106 2FKA BEF 0.00589 0.45798 18.6047
107 2TPI ILE VAL 0.03161 0.40066 18.7773
108 1UGY GLA BGC 0.0169 0.42654 20
109 2BOS GLA GAL 0.01159 0.41178 29.4118
110 4M1U A2G MBG 0.01921 0.42148 30
Pocket No.: 2; Query (leader) PDB : 1REQ; Ligand: DCA; Similar sites found: 19
This union binding pocket(no: 2) in the query (biounit: 1req.bio1) has 43 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1OFL NGK GCD 0.04801 0.40862 1.8711
2 2VQ5 HBA 0.03195 0.41309 2.98507
3 3JU6 ANP 0.001998 0.48748 3.24324
4 1S5O 152 0.01888 0.43593 3.57143
5 2BMB PMM 0.04802 0.40059 4.40367
6 3GM5 CIT 0.009758 0.44625 5.03145
7 1GPM CIT 0.03822 0.41693 5.33333
8 2CI5 HCS 0.04273 0.40607 5.6338
9 1EPB REA 0.012 0.42444 6.70732
10 1VKF CIT 0.04372 0.41131 6.91489
11 3LGS SAH 0.04835 0.40044 7.49064
12 2ZMF CMP 0.0219 0.40543 9.52381
13 4EE7 PIS 0.009099 0.44111 9.53947
14 5KY9 GDP 0.03746 0.40301 11.5493
15 2VFT SOR 0.02031 0.42375 12.0853
16 2OMN IPH 0.03019 0.40039 14.7465
17 2YIP YIO 0.01138 0.44694 15.942
18 5KEW 6SB 0.04952 0.40666 15.9574
19 1RZX ACE VAL LYS GLU SER LEU VAL 0.03666 0.41943 20.4082
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