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 Z2691943589

PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak SASA cached

Weak or marginal quality

Binding strong Geometry medium Native strong SASA done

Strain ΔE

33.6 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.47, Jaccard 0.35, H-bond role recall 0.60

Burial

74%

Hydrophobic fit

72%

Reason: no major geometry red flags detected

3 protein-contact clashes 3 intramolecular clashes 93% of hydrophobic surface is solvent-exposed (13/14 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.

Molecular report

Full metrics ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-1.045 kcal/mol/HA) ✓ Good fit quality (FQ -9.22) ✓ Good H-bonds (5 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Very high strain energy (33.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)

Score

-24.033

kcal/mol

-1.045

kcal/mol/HA

Fit Quality

-9.22

FQ (Leeson)

HAC

heavy atoms

332

LogP

-2.93

cLogP

Final rank

4.5256

rank score

Inter norm

-0.952

normalised

Contacts

H-bonds 10

Strain ΔE

33.6 kcal/mol

SASA buried

74%

Lipo contact

72% BSA apolar/total

SASA unbound

549 Å²

Apolar buried

294 Å²

Interaction summary

HBD 3 HBA 2 HY 3 PI 0 CLASH 3

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: 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	7	Native recall	0.47
Jaccard	0.35	RMSD	-
HB strict	2	Strict recall	0.33
HB same residue+role	3	HB role recall	0.60
HB same residue	3	HB residue recall	0.60

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
415	4.525565322858871	-0.952208	-24.0333	10	12	7	0.47	0.60	-	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 -24.033kcal/mol

Ligand efficiency (LE) -1.0449kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.222

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

Heavy atom count 23HA

Physicochemical properties

Molecular weight 332.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) -2.93

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 33.59kcal/mol

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

Docked FF energy 208.59kcal/mol

Minimised FF energy 175.00kcal/mol

SASA & burial

✓ computed

SASA (unbound) 549.2Å²

Total solvent-accessible surface area of free ligand

BSA total 408.9Å²

Buried surface area upon binding

BSA apolar 293.9Å²

Hydrophobic contacts buried

BSA polar 115.0Å²

Polar contacts buried

Fraction buried 74.4%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 71.9%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2397.3Å²

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 1367.3Å²

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