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_Schistosoma_102

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

50.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

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

Burial

72%

Hydrophobic fit

90%

Reason: strain 50.2 kcal/mol

strain ΔE 50.2 kcal/mol 2 protein-contact clashes 91% of hydrophobic surface is solvent-exposed (32/35 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. 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 Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.426 kcal/mol/HA) ✓ Good fit quality (FQ -4.66) ✓ Good H-bonds (3 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (90%) ✗ Extreme strain energy (50.2 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (20)

Score

-20.881

kcal/mol

-0.426

kcal/mol/HA

Fit Quality

-4.66

FQ (Leeson)

HAC

heavy atoms

707

LogP

4.29

cLogP

Final rank

2.7462

rank score

Inter norm

-0.484

normalised

Contacts

H-bonds 3

Strain ΔE

50.2 kcal/mol

SASA buried

72%

Lipo contact

90% BSA apolar/total

SASA unbound

1054 Å²

Apolar buried

684 Å²

Interaction summary

HBD 1 HBA 2 HY 3 PI 0 CLASH 2

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	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
41	2.746227812516877	-0.483747	-20.8815	3	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 -20.881kcal/mol

Ligand efficiency (LE) -0.4262kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -4.663

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

Heavy atom count 49HA

Physicochemical properties

Molecular weight 706.7Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.29

Lipinski: ≤ 5

Rotatable bonds 11

Conformational strain (MMFF94s)

Strain energy (ΔE) 50.20kcal/mol

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

Docked FF energy 204.89kcal/mol

Minimised FF energy 154.69kcal/mol

SASA & burial

✓ computed

SASA (unbound) 1053.8Å²

Total solvent-accessible surface area of free ligand

BSA total 761.2Å²

Buried surface area upon binding

BSA apolar 684.2Å²

Hydrophobic contacts buried

BSA polar 77.0Å²

Polar contacts buried

Fraction buried 72.2%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 89.9%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2853.3Å²

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 1442.2Å²

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