FAIRMol

OHD_MAC_49

Pose ID 9167 Compound 589 Pose 359

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
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_MAC_49
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
34.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.60, Jaccard 0.36, H-bond role recall 0.40
Burial
81%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 41% of hydrophobic surface appears solvent-exposed (9/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.653 kcal/mol/HA) ✓ Good fit quality (FQ -6.48) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Very high strain energy (34.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-21.558
kcal/mol
LE
-0.653
kcal/mol/HA
Fit Quality
-6.48
FQ (Leeson)
HAC
33
heavy atoms
MW
447
Da
LogP
2.78
cLogP
Strain ΔE
34.3 kcal/mol
SASA buried
81%
Lipo contact
82% BSA apolar/total
SASA unbound
743 Ų
Apolar buried
495 Ų

Interaction summary

HB 7 HY 20 PI 0 CLASH 3 ⚠ Exposure 40%
⚠️Partial hydrophobic solvent exposure
41% of hydrophobic surface appears solvent-exposed (9/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 22 Buried (contacted) 13 Exposed 9 LogP 2.78 H-bonds 7
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (2/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank3.980Score-21.558
Inter norm-0.750Intra norm0.097
Top1000noExcludedno
Contacts19H-bonds7
Artifact reasongeometry warning; 13 clashes; 2 protein clashes; high strain Δ 34.3
Residues
ARG22 ARG342 CYS26 GLN341 GLU343 GLU384 LEU25 LEU339 LEU350 LEU372 LEU382 PRO338 PRO340 PRO344 PRO373 THR21 THR285 TYR370 TYR371

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL: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

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap9Native recall0.60
Jaccard0.36RMSD-
HB strict2Strict recall0.33
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
358 1.0155874823896842 -1.03757 -29.1722 9 19 0 0.00 0.00 - no Open
429 1.2454421783000702 -0.93846 -24.4127 5 19 0 0.00 0.00 - no Open
313 2.885852622249077 -1.01039 -27.4889 13 18 0 0.00 0.00 - no Open
398 2.924227394629478 -0.835383 -20.9815 7 17 0 0.00 0.00 - no Open
352 3.0026657423916276 -0.732155 -19.3364 5 17 0 0.00 0.00 - no Open
380 3.3276613975301435 -0.663488 -20.2658 8 17 0 0.00 0.00 - no Open
445 3.555221163076815 -0.895338 -24.4953 7 23 0 0.00 0.00 - no Open
474 3.58031970662104 -0.827347 -20.0987 7 20 0 0.00 0.00 - no Open
359 3.979795137275888 -0.749907 -21.5576 7 19 9 0.60 0.40 - no Current
449 4.019285786281364 -0.837107 -23.0178 9 20 0 0.00 0.00 - no Open
339 4.480605875198744 -0.932411 -28.9537 15 24 0 0.00 0.00 - no Open
412 4.730901331874943 -0.778603 -23.0559 9 17 0 0.00 0.00 - no Open
374 5.169873192086845 -0.788752 -19.2509 8 18 0 0.00 0.00 - no Open
369 5.306786399993182 -0.810316 -22.4469 16 17 0 0.00 0.00 - no Open
315 6.093306122153872 -0.830242 -14.8988 12 20 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 -21.558kcal/mol
Ligand efficiency (LE) -0.6533kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.482
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 447.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.78
Lipinski: ≤ 5
Rotatable bonds 11

Conformational strain (MMFF94s)
Strain energy (ΔE) 34.30kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 109.75kcal/mol
Minimised FF energy 75.45kcal/mol

SASA & burial

✓ computed
SASA (unbound) 742.5Ų
Total solvent-accessible surface area of free ligand
BSA total 604.0Ų
Buried surface area upon binding
BSA apolar 495.3Ų
Hydrophobic contacts buried
BSA polar 108.7Ų
Polar contacts buried
Fraction buried 81.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2562.2Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1381.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)