Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T14

T. brucei ODC (G418 binding site) T. brucei G418 binding site

Ligand KB_HAT_99

PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Reject SASA cached

Likely artefact or unreliable pose

Binding strong Geometry medium Native mixed SASA done

Strain ΔE

39.6 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.53, Jaccard 0.44, H-bond role recall 0.00

Burial

74%

Hydrophobic fit

77%

Reason: no major geometry red flags detected

5 protein-contact clashes 5 intramolecular clashes 58% of hydrophobic surface appears solvent-exposed (11/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Not classified (>100 mg/L)

Daphnia EC₅₀

Not classified (>100 mg/L)

Algae IC₅₀

Not classified (>100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.701 kcal/mol/HA) ✓ Good fit quality (FQ -6.70) ✓ Good H-bonds (3 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Very high strain energy (39.6 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (9) ✗ Many internal clashes (13)

Score

-20.338

kcal/mol

-0.701

kcal/mol/HA

Fit Quality

-6.70

FQ (Leeson)

HAC

heavy atoms

415

LogP

1.91

cLogP

Final rank

2.1531

rank score

Inter norm

-0.769

normalised

Contacts

H-bonds 4

Strain ΔE

39.6 kcal/mol

SASA buried

74%

Lipo contact

77% BSA apolar/total

SASA unbound

684 Å²

Apolar buried

389 Å²

Interaction summary

HBA 3 HY 3 PI 0 CLASH 5

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

PI · π–π interactions

No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference

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

Name	1NJJ	Contacts	15
Pose	Open native pose	HB	0
IFP residues	ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap	8	Native recall	0.53
Jaccard	0.44	RMSD	-
HB strict	0	Strict recall	0.00
HB same residue+role	0	HB role recall	0.00
HB same residue	2	HB residue recall	0.40

Protein summary

398 residues

Protein target	T14	Atoms	6140
Residues	398	Chains	1
Residue summary	VAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

Receptor context

1 kept / 0 excluded

Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.

Kept context 1 Excluded HETATM 0

Kept cofactors / ions

A:ORX602

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
136	2.1531470140754565	-0.76944	-20.3379	4	11	8	0.53	0.00	-	no	Current
69	5.171372753763336	-1.05819	-29.359	13	22	0	0.00	0.00	-	no	Open

Molecular metrics

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

✓ Metrics available

Scoring & efficiency

Docking score -20.338kcal/mol

Ligand efficiency (LE) -0.7013kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.695

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

Heavy atom count 29HA

Physicochemical properties

Molecular weight 415.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 1.91

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 39.58kcal/mol

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

Docked FF energy 80.11kcal/mol

Minimised FF energy 40.53kcal/mol

SASA & burial

✓ computed

SASA (unbound) 684.5Å²

Total solvent-accessible surface area of free ligand

BSA total 503.4Å²

Buried surface area upon binding

BSA apolar 388.7Å²

Hydrophobic contacts buried

BSA polar 114.6Å²

Polar contacts buried

Fraction buried 73.5%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 77.2%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2491.0Å²

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 3349.0Å²

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

Complex non-polar SASA 1380.9Å²

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