Ligand clusters for UniProt code P06746

Ligand clusters for P06746: DNA polymerase beta from Homo sapiens

		Top 6 (of 57) ligand clusters Cluster 1. 91 ligand types 1044 ligands Cluster 2. 5 ligand types 13 ligands Cluster 3. 3 ligand types 3 ligands Cluster 4. 4 ligand types 12 ligands Cluster 5. 3 ligand types 3 ligands Cluster 6. 3 ligand types 6 ligands
Representative protein: 4rq2A

Structures

PDB		Schematic diagram
4rq2A
5tb9A
3isdA
5bpcA
4kldA
		more ...

Cluster 1 contains 91 ligand types (of which only 20 are listed. Click for all)

Use checkboxes to select ligands to display in RasMol, Jmol, or download as an SDF file. Selection shortcuts: select all/none invert selection.
Ligand		Description
_Mg		1. Metal: _MG × 185 PDB codes: 1bpy(A), 1mq3(A), 1zjn(A), 2fmp(A), 2fmq(A), 2fms(A), 2iso(A), 2isp(A), 2pxi(A), 3gdx(A), 3jpn(A), 3jpo(A), 3jpp(A), 3jpq(A), 3jpr(A), 3jps(A), 3jpt(A), 3lk9(A), 3mby(A), 3rjf(A), 3rjh(A), 3rji(A), 3rjk(A), 3tfr(A), 3tfs(A), 4do9(A), 4doa(A), 4dob(A), 4doc(A), 4f5o(A), 4f5p(A), 4jwm(A), 4jwn(A), 4kle(A), 4klf(A), 4klg(A), 4kli(A), 4klj(A), 4kll(A), 4klm(A), 4klo(A), 4m47(A), 4m9j(A), 4m9l(A), 4m9n(A), 4mfa(A), 4mfc(A), 4mff(A), 4nlk(A), 4nln(A), 4nm1(A), 4o5e(A), 4o5k(A), 4pgq(A), 4ph5(A), 4pha(A), 4phe(A), 4r65(A), 4rpy(A), 4rpz(A), 4rq0(A), 4rq4(A), 4rq5(A), 4rq6(A), 4rt2(A), 4rt3(A), 4tuq(A), 4tur(A), 4uay(A), 4uaz(A), 4ub3(A), 4ubb(A), 4ymn(A), 4z6c(A), 4z6d(A), 5bol(A), 5eoz(A), 5j29(A), 5j2a(A), 5j2b(A), 5j2c(A), 5j2d(A), 5j2e(A), 5j2f(A), 5j2g(A), 5j2h(A), 5j2i(A), 5j2j(A), 5j2k(A), 5ugn(A), 5ugp(A), 5vry(A), 5vrz(A), 5vs0(A), 5vs3(A), 5vs4(A), 6btf(A), 6cpq(A), 6cr3(A), 6cr4(A), 6cr5(A), 6cr6(A), 6cr7(A), 6cr8(A), 6cr9(A), 6crb(A), 6crc(A), 6cti(A), 6ctj(A), 6ctk(A), 6ctl(A), 6ctm(A), 6ctn(A), 6cto(A), 6ctp(A), 6e3v(A), 6e3w(A), 6e3x(A), 6g2q(A), 6n2s(A), 6n2t(A), 8ici(A), 9icn(A).
_Mn		2. Metal: _MN × 121 PDB codes: 1zql(A), 1zqm(A), 1zqq(A), 3c2k(A), 3c2l(A), 3c2m(A), 3isd(A), 3rh4(A), 3rh5(A), 3rh6(A), 4f5q(A), 4gxj(A), 4gxk(A), 4klh(A), 4klq(A), 4kls(A), 4klt(A), 4lvs(A), 4nxz(A), 4ny8(A), 4p2h(A), 4pgx(A), 4phd(A), 4php(A), 4r66(A), 4rq2(A), 4rq8(A), 4tus(A), 4ub5(A), 4ymo(A), 4yn4(A), 4z6e(A), 4z6f(A), 5bpc(A), 5tb8(A), 5tb9(A), 5tbb(A), 5u9h(A), 6cu9(A), 6cua(A), 6cub(A), 6u6b(A), 6uok(F), 6uol(A), 6uom(A), 7k97(A), 8ick(A), 8icn(A), 8ico(A), 8icp(A), 8icr(A), 8ics(A), 8ict(A), 8icu(A), 8icv(A), 8icw(A), 8icx(A), 8icy(A), 9ica(A), 9icl(A), 9icq(A), 9icr(A), 9ics(A), 9ict(A), 9icu(A).
		3. Ligand: PPV × 35 pyrophosphoric acid Pyrophosphate PDB codes: 4kle(A), 4klf(A), 4klg(A), 4klh(A), 4kli(A), 4klj(A), 4kll(A), 4klm(A), 4klo(A), 4klq(A), 4kls(A), 4klt(A), 4rpy(A), 4rpz(A), 4rq0(A), 4rq2(A), 4rq4(A), 4rq5(A), 4rq6(A), 4rq8(A), 4uay(A), 4uaz(A), 4ub3(A), 4ubb(A), 5tba(A), 5tbb(A), 5u9h(A), 5v1i(A), 5v1o(A), 5v1r(A), 5vry(A), 5vrz(A), 5vs0(A), 5vs3(A), 5vs4(A).
_Zn		4. Metal: _ZN × 12 PDB codes: 1zqt(A), 7ico(A), 7icp(A), 7icr(A), 9icf(A), 9icg(A), 9ich(A), 9ici(A), 9icv(A),
__K		5. Metal: __K × 4 PDB codes: 1zqa(A), 1zqi(A), 1zqk(A), 1zqp(A).
_Na		6. Metal: _NA × 371 PDB codes: 1bpx(A), 1bpy(A), 1bpz(A), 1mq2(A), 1mq3(A), 1tv9(A), 1tva(A), 1zjm(A), 1zjn(A), 1zqg(A), 1zqh(A), 1zqo(A), 1zqq(A), 1zqr(A), 1zqs(A), 1zqt(A), 2fmp(A), 2fmq(A), 2fms(A), 2i9g(A), 2iso(A), 2isp(A), 2p66(A), 2pxi(A), 3c2k(A), 3c2l(A), 3c2m(A), 3gdx(A), 3isb(A), 3isc(A), 3isd(A), 3jpo(A), 3jpp(A), 3jpq(A), 3jpr(A), 3jps(A), 3jpt(A), 3lk9(A), 3mby(A), 3ogu(A), 3rh4(A), 3rh5(A), 3rh6(A), 3rje(A), 3rjf(A), 3rjg(A), 3rjh(A), 3rji(A), 3rjj(A), 3rjk(A), 3tfr(A), 3tfs(A), 4do9(A), 4doa(A), 4dob(A), 4doc(A), 4f5n(A), 4f5p(A), 4f5q(A), 4f5r(A), 4gxi(A), 4gxj(A), 4gxk(A), 4jwm(A), 4jwn(A), 4kld(A), 4klf(A), 4klg(A), 4klh(A), 4kli(A), 4klj(A), 4kll(A), 4klm(A), 4klo(A), 4klq(A), 4kls(A), 4klt(A), 4klu(A), 4lvs(A), 4m2y(A), 4m47(A), 4m9g(A), 4m9h(A), 4m9j(A), 4m9l(A), 4m9n(A), 4mf2(A), 4mf8(A), 4mfa(A), 4mfc(A), 4mff(A), 4nlk(A), 4nln(A), 4nlz(A), 4nm1(A), 4nm2(A), 4nxz(A), 4ny8(A), 4o5c(A), 4o5e(A), 4o5k(A), 4o9m(A), 4p2h(A), 4pgq(A), 4pgx(A), 4ph5(A), 4pha(A), 4phd(A), 4phe(A), 4php(A), 4ppx(A), 4r63(A), 4r64(A), 4r65(A), 4r66(A), 4rpx(A), 4rpy(A), 4rpz(A), 4rq0(A), 4rq1(A), 4rq2(A), 4rq3(A), 4rq4(A), 4rq5(A), 4rq6(A), 4rq7(A), 4rq8(A), 4rt2(A), 4rt3(A), 4tup(A), 4tuq(A), 4tur(A), 4tus(A), 4uaw(A), 4uay(A), 4ub3(A), 4ub5(A), 4ymm(A), 4ymn(A), 4ymo(A), 4yn4(A), 4z6c(A), 4z6d(A), 4z6e(A), 4z6f(A), 5bol(A), 5bom(A), 5bpc(A), 5db6(A), 5db7(A), 5db8(A), 5db9(A), 5dba(A), 5dbb(A), 5dbc(A), 5eoz(A), 5hhh(A), 5hhi(A), 5j0o(A), 5j0p(A), 5j0q(A), 5j0r(A), 5j0s(A), 5j0t(A), 5j0u(A), 5j0v(A), 5j0w(A), 5j0x(A), 5j0y(A), 5j29(A), 5j2a(A), 5j2b(A), 5j2c(A), 5j2d(A), 5j2e(A), 5j2f(A), 5j2g(A), 5j2h(A), 5j2i(A), 5j2j(A), 5j2k(A), 5tb8(A), 5tb9(A), 5tba(A), 5tbb(A), 5tbc(A), 5tzv(A), 5u2r(A), 5u2s(A), 5u2t(A), 5u8g(A), 5u8h(A), 5u8i(A), 5u9h(A), 5v1j(A), 5wnx(A), 5wny(A), 5wnz(A), 5wo0(A), 6bte(A), 6btf(A), 6cly(A), 6cpq(A), 6cr3(A), 6cr4(A), 6cr5(A), 6cr6(A), 6cr7(A), 6cr8(A), 6cr9(A), 6crb(A), 6crc(A), 6cti(A), 6ctj(A), 6ctk(A), 6ctl(A), 6ctm(A), 6ctn(A), 6cto(A), 6ctp(A), 6cu9(A), 6cua(A), 6cub(A), 6dia(A), 6dic(A), 6e3r(A), 6e3v(A), 6e3w(A), 6e3x(A), 6g2q(A), 6mr7(A), 6mr8(A), 6n2r(A), 6n2t(A), 6ph5(A), 7ice(A), 7icf(A), 7icg(A), 7ich(A), 7ici(A), 7ick(A), 7icl(A), 7icm(A), 7icn(A), 7ico(A), 7icp(A), 7icq(A), 7icr(A), 7ics(A), 7ict(A), 7icu(A), 7icv(A), 8ica(A), 8icb(A), 8icc(A), 8ice(A), 8icf(A), 8icg(A), 8ich(A), 8ici(A), 8icj(A), 8ick(A), 8icl(A), 8icm(A), 8icn(A), 8ico(A), 8icp(A), 8icq(A), 8icr(A), 8ics(A), 8ict(A), 8icu(A), 8icv(A), 8icw(A), 8icx(A), 8icy(A), 8icz(A), 9icb(A), 9icc(A), 9ice(A), 9icf(A), 9icg(A), 9ich(A), 9ici(A), 9icj(A), 9ick(A), 9icl(A), 9icm(A), 9icn(A), 9ico(A), 9icp(A), 9icq(A), 9icr(A), 9ics(A), 9ict(A), 9icu(A), 9icv(A), 9icw(A), 9icx(A), 9icy(A).
_Ca		7. Metal: _CA × 48 PDB codes: 1zqc(A), 1zqd(A), 1zqj(A), 4kld(A), 4rpx(A), 4rq3(A), 4uaw(A), 4ub4(A), 4ubc(A), 5u2r(A), 5u2s(A), 5u2t(A), 5ugo(A), 5vrw(A), 5vrx(A), 5vs1(A), 5vs2(A), 5wnx(A), 5wny(A), 5wnz(A), 5wo0(A), 6dia(A), 6dic(A), 6mr7(A), 6mr8(A), 8ica(A).
		8. Ligand: DUP × 21 2'-Deoxyuridine 5'-Alpha,Beta-Imido-Triphosphate PDB codes: 2fmq(A), 2fms(A), 3c2k(A), 4jwm(A), 4jwn(A), 4m9j(A), 4r65(A), 4r66(A), 5j29(A), 5j2a(A), 5j2b(A), 5j2c(A), 5j2d(A), 5j2e(A), 5j2f(A), 5j2g(A), 5j2h(A), 5j2i(A), 5j2j(A), 5j2k(A), 6btf(A).
		9. Ligand: DTP × 20 2'-Deoxyadenosine 5'-Triphosphate PDB codes: 4klq(A), 4kls(A), 4lvs(A), 4m9n(A), 4rq3(A), 4rq4(A), 4rq5(A), 6cr4(A), 8ica(A), 8ice(A), 8icf(A), 8ick(A), 8icl(A), 8icp(A), 8icr(A), 9icb(A), 9icc(A), 9icf(A), 9icq(A), 9icv(A).
		10. Ligand: DCP × 17 2'-Deoxycytidine-5'-Triphosphate PDB codes: 1mq3(A), 3rh5(A), 4kld(A), 4kle(A), 4klf(A), 4m9l(A), 4rpx(A), 4rpy(A), 4rpz(A), 5v1f(A), 5v1n(A), 5v1r(A), 6ph6(A), 8ics(A), 8ict(A), 9icg(A), 9icr(A).
		11. Ligand: 0KX × 15 2'-Deoxy-5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine PDB codes: 4mfc(A), 4nlk(A), 4ny8(A), 4o5k(A), 4pha(A), 4phd(A), 4tuq(A), 4tur(A), 4tus(A), 4ymn(A), 4ymo(A), 4z6c(A), 5eoz(A), 6cpq(A), 6cu9(A).
		12. Ligand: TTP × 13 Thymidine-5'-Triphosphate PDB codes: 4m9h(A), 5vrw(A), 5vrx(A), 5vry(A), 5vrz(A), 5vs1(A), 5vs2(A), 5vs3(A), 8icj(A), 8icw(A), 8icx(A), 8icy(A), 9icu(A).
		13. Ligand: 1FZ × 11 5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]thymidine PDB codes: 4mff(A), 4nxz(A), 4o5e(A), 4p2h(A), 4pgq(A), 4pgx(A), 4yn4(A), 4z6d(A), 4z6e(A), 4z6f(A), 6e3v(A).
		14. Ligand: PO4 × 10 Phosphate ion PDB codes: 1tv9(A), 1tva(A), 2p66(A), 4mf8(A), 4mfa(A), 4nln(A), 4nlz(A), 4nm1(A), 4ph5(A), 7k97(A).
		15. Ligand: 6CF × 8 2'-Deoxy-5'-O-[(S)-{Difluoro[(s)- Hydroxy(phosphonooxy) phosphoryl]methyl}(hydroxy)phosphoryl]cytidine PDB codes: 3rjh(A), 3rji(A), 3rjk(A), 4f5n(A), 4f5o(A), 4f5q(A), 4f5r(A), 4gxj(A).
		16. Ligand: DGT × 8 2'-Deoxyguanosine-5'-Triphosphate PDB codes: 1zjn(A), 4ub4(A), 6nkr(A), 6nku(A), 6nkx(A), 8icv(A), 9ich(A), 9ict(A).
		17. Ligand: F2A × 7 2'-Deoxy-5'-O-[(S)-Hydroxy{[(s)-Hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]adenosine PDB codes: 3c2l(A), 3c2m(A), 3isd(A), 3rjf(A), 4f5p(A), 4gxk(A), 5bpc(A).
		18. Ligand: XG4 × 7 2'-Deoxy-5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]guanosine PDB codes: 4m47(A), 4phe(A), 4php(A), 6crh(A), 6cua(A), 6e3w(A), 6pkz(A).
		19. Ligand: 8DG × 6 8-Oxo-2'-Deoxyguanosine-5'-Triphosphate PDB codes: 3mby(A), 4uaw(A), 4uaz(A), 4ub5(A), 4ubb(A), 4ubc(A).
_Cl		20. Metal: _CL × 6 PDB codes: 4rq8(A), 5j2d(A), 5j2e(A), 5j2f(A), 5j2g(A), 5j2h(A).
+ more. Press for full list

Cluster 2 contains 5 ligand types

Selection shortcuts: select all/none invert selection.
Ligand		Description
		1. Ligand: IMD × 4 Imidazole PDB codes: 5vrx(A), 5vry(A), 5vrz(A), 5vs0(A).
		2. Ligand: ACT × 3 Acetate ion PDB codes: 5u2r(A), 5vs3(A), 5vs4(A).
		3. Ligand: PEG × 3 Di(hydroxyethyl)ether PDB codes: 5vrw(A), 5vrx(A), 5vs1(A).
		4. Ligand: CTP × 2 Cytidine-5'-Triphosphate PDB codes: 3rh4(A), 3rh6(A).
		5. Ligand: DCP × 1 2'-Deoxycytidine-5'-Triphosphate PDB code: 3rh5(A).

Cluster 3 contains 3 ligand types

Selection shortcuts: select all/none invert selection.
Ligand		Description
		1. Ligand: 2RW × 1 [(2r,3s,4r,5r)-5-(6-Amino-9h-Purin-9-Yl)-3,4- Dihydroxytetrahydrofuran-2-Yl]methyl [(2r,3s)-3- Hydroxytetrahydrofuran-2-Yl]methyl dihydrogen diphosphate PDB code: 4o9m(A).
		2. Ligand: ACT × 1 Acetate ion PDB code: 4rpx(A).
		3. Ligand: EDO × 1 1,2-Ethanediol PDB code: 6uom(A).

Cluster 4 contains 4 ligand types

Selection shortcuts: select all/none invert selection.
Ligand		Description
_Mn		1. Metal: _MN × 8 PDB codes: 3c2l(A), 3c2m(A), 3isd(A), 4gxk(A), 4klt(A), 4lvs(A), 6uok(F), 7k97(A).
		2. Ligand: EDO × 2 1,2-Ethanediol PDB codes: 3c2m(A), 3isd(A).
		3. Ligand: ACT × 1 Acetate ion PDB code: 5tb8(A).
		4. Ligand: DCP × 1 2'-Deoxycytidine-5'-Triphosphate PDB code: 4rq0(A).

Cluster 5 contains 3 ligand types

Selection shortcuts: select all/none invert selection.
Ligand		Description
		1. Ligand: ACT × 1 Acetate ion PDB code: 4rq6(A).
		2. Ligand: EDO × 1 1,2-Ethanediol PDB code: 6uol(A).
		3. Ligand: MES × 1 2-(N-Morpholino)-Ethanesulfonic acid PDB code: 3ogu(A).

Cluster 6 contains 3 ligand types

Selection shortcuts: select all/none invert selection.
Ligand		Description
_Mn		1. Metal: _MN × 4 PDB codes: 4rq2(A), 4rq8(A), 5tb8(A), 5tb9(A).
		2. Ligand: ACT × 1 Acetate ion PDB code: 4rq3(A).
		3. Ligand: PEG × 1 Di(hydroxyethyl)ether PDB code: 5vrw(A).