Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T13

T. brucei ODC (Active site) T. brucei Active site

Ligand Z56775559

PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Reject SASA cached

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

51.1 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.58, Jaccard 0.38, H-bond role recall 0.29

Burial

74%

Hydrophobic fit

80%

Reason: strain 51.1 kcal/mol

strain ΔE 51.1 kcal/mol 1 protein-contact clashes 50% of hydrophobic surface appears solvent-exposed (16/32 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Daphnia EC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Algae IC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG High Ames Clear DILI Low

Molecular report

Full metrics ↗

Reject Multiple quality flags — this pose should be deprioritised or discarded.

✓ Excellent LE (-0.451 kcal/mol/HA) ✓ Good fit quality (FQ -4.81) ✓ Good H-bonds (5 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (51.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (21)

Score

-19.821

kcal/mol

-0.451

kcal/mol/HA

Fit Quality

-4.81

FQ (Leeson)

HAC

heavy atoms

595

LogP

3.94

cLogP

Final rank

4.1068

rank score

Inter norm

-0.695

normalised

Contacts

H-bonds 8

Strain ΔE

51.1 kcal/mol

SASA buried

74%

Lipo contact

80% BSA apolar/total

SASA unbound

942 Å²

Apolar buried

555 Å²

Interaction summary

HBD 1 HBA 4 HY 4 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

PI · π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference

Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.

Name	1F3T	Contacts	19
Pose	Open native pose	HB	0
IFP residues	ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap	11	Native recall	0.58
Jaccard	0.38	RMSD	-
HB strict	1	Strict recall	0.11
HB same residue+role	2	HB role recall	0.29
HB same residue	2	HB residue recall	0.29

Protein summary

411 residues

Protein target	T13	Atoms	6340
Residues	411	Chains	1
Residue summary	VAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
604	2.7675540002054433	-0.479909	-24.179	3	18	0	0.00	0.00	-	no	Open
593	4.106760461201954	-0.694753	-19.8214	8	21	11	0.58	0.29	-	no	Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -19.821kcal/mol

Ligand efficiency (LE) -0.4505kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -4.813

LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe

Heavy atom count 44HA

Physicochemical properties

Molecular weight 594.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.94

Lipinski: ≤ 5

Rotatable bonds 10

Conformational strain (MMFF94s)

Strain energy (ΔE) 51.07kcal/mol

< 5 good · 5–10 marginal · > 10 problematic

Docked FF energy 257.30kcal/mol

Minimised FF energy 206.23kcal/mol

SASA & burial

✓ computed

SASA (unbound) 942.2Å²

Total solvent-accessible surface area of free ligand

BSA total 697.0Å²

Buried surface area upon binding

BSA apolar 555.4Å²

Hydrophobic contacts buried

BSA polar 141.6Å²

Polar contacts buried

Fraction buried 74.0%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 79.7%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2816.4Å²

SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.

Receptor non-polar SASA 3461.2Å²

Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)

Complex non-polar SASA 1396.7Å²

Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)