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 OHD_TC1_242

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

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

43.5 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.80, Jaccard 0.57, H-bond role recall 0.20

Burial

70%

Hydrophobic fit

95%

Reason: strain 43.5 kcal/mol

strain ΔE 43.5 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 65% of hydrophobic surface is solvent-exposed (28/43 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Daphnia EC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Algae IC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Bioaccum.

vB — Very bioaccumulative (BCF>5000)

Persistent

Yes

ADMET alerts (in-silico)

hERG High Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Good LE (-0.347 kcal/mol/HA) ✓ Good fit quality (FQ -3.78) ✓ Good H-bonds (3 bonds) ✓ Deep burial (70% SASA buried) ✓ Lipophilic contacts well-matched (95%) ✗ Extreme strain energy (43.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)

Score

-16.643

kcal/mol

-0.347

kcal/mol/HA

Fit Quality

-3.78

FQ (Leeson)

HAC

heavy atoms

657

LogP

6.76

cLogP

Final rank

3.5430

rank score

Inter norm

-0.504

normalised

Contacts

H-bonds 4

Strain ΔE

43.5 kcal/mol

SASA buried

70%

Lipo contact

95% BSA apolar/total

SASA unbound

978 Å²

Apolar buried

648 Å²

Interaction summary

HBD 3 HY 3 PI 0 CLASH 3

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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: strict.

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	12	Native recall	0.80
Jaccard	0.57	RMSD	-
HB strict	1	Strict recall	0.17
HB same residue+role	1	HB role recall	0.20
HB same residue	1	HB residue recall	0.20

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
112	3.543016068334288	-0.504479	-16.6432	4	18	12	0.80	0.20	-	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 -16.643kcal/mol

Ligand efficiency (LE) -0.3467kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -3.777

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

Heavy atom count 48HA

Physicochemical properties

Molecular weight 657.0Da

Lipinski: ≤ 500 Da

LogP (cLogP) 6.76

Lipinski: ≤ 5

Rotatable bonds 10

Conformational strain (MMFF94s)

Strain energy (ΔE) 43.51kcal/mol

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

Docked FF energy 249.44kcal/mol

Minimised FF energy 205.93kcal/mol

SASA & burial

✓ computed

SASA (unbound) 977.8Å²

Total solvent-accessible surface area of free ligand

BSA total 682.8Å²

Buried surface area upon binding

BSA apolar 647.9Å²

Hydrophobic contacts buried

BSA polar 34.9Å²

Polar contacts buried

Fraction buried 69.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 94.9%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2883.8Å²

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 1374.6Å²

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