FAIRMol

OHD_TB2021_76

Pose ID 8878 Compound 4107 Pose 70

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_TB2021_76
PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native mixed SASA done
Strain ΔE
13.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.47, Jaccard 0.37, H-bond role recall 0.00
Burial
73%
Hydrophobic fit
77%
Reason: no major geometry red flags detected
1 protein-contact clashes 39% of hydrophobic surface appears solvent-exposed (7/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.984 kcal/mol/HA) ✓ Good fit quality (FQ -8.68) ✓ Good H-bonds (4 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Moderate strain (13.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-22.620
kcal/mol
LE
-0.984
kcal/mol/HA
Fit Quality
-8.68
FQ (Leeson)
HAC
23
heavy atoms
MW
303
Da
LogP
2.51
cLogP
Strain ΔE
13.8 kcal/mol
SASA buried
73%
Lipo contact
77% BSA apolar/total
SASA unbound
553 Ų
Apolar buried
309 Ų

Interaction summary

HB 4 HY 3 PI 0 CLASH 1 ⚠ Exposure 38%
⚠️Partial hydrophobic solvent exposure
39% of hydrophobic surface appears solvent-exposed (7/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 18 Buried (contacted) 11 Exposed 7 LogP 2.51 H-bonds 4
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank1.737Score-22.620
Inter norm-0.949Intra norm-0.035
Top1000noExcludedno
Contacts11H-bonds4
Artifact reasongeometry warning; 9 clashes; 1 protein clash
Residues
ALA334 ARG242 ARG337 ASP243 ASP385 GLU384 LEU339 PHE383 THR241 VAL335 VAL336

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 overlap7Native recall0.47
Jaccard0.37RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue1HB residue recall0.20

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
70 1.736716694845178 -0.948783 -22.6203 4 11 7 0.47 0.00 - no Current
65 2.976826282107063 -0.845128 -19.5223 5 9 0 0.00 0.00 - no Open
36 3.3707797679056615 -1.3162 -25.7605 6 17 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 -22.620kcal/mol
Ligand efficiency (LE) -0.9835kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.680
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 303.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.51
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 148.62kcal/mol
Minimised FF energy 134.79kcal/mol

SASA & burial

✓ computed
SASA (unbound) 553.2Ų
Total solvent-accessible surface area of free ligand
BSA total 403.4Ų
Buried surface area upon binding
BSA apolar 308.8Ų
Hydrophobic contacts buried
BSA polar 94.6Ų
Polar contacts buried
Fraction buried 72.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2398.0Ų
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 1406.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)