FAIRMol

OHD_ACDS_35

Pose ID 8804 Compound 898 Pose 674

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
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand OHD_ACDS_35
PDB1F3T↗

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
48.2 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.84, Jaccard 0.76, H-bond role recall 0.14
Burial
74%
Hydrophobic fit
91%
Reason: strain 48.2 kcal/mol
strain ΔE 48.2 kcal/mol 5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.806 kcal/mol/HA) ✓ Good fit quality (FQ -8.00) ✓ Good H-bonds (3 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (91%) ✗ Extreme strain energy (48.2 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (9) ✗ Many internal clashes (14)
Score
-26.599
kcal/mol
LE
-0.806
kcal/mol/HA
Fit Quality
-8.00
FQ (Leeson)
HAC
33
heavy atoms
MW
569
Da
LogP
6.90
cLogP
Strain ΔE
48.2 kcal/mol
SASA buried
74%
Lipo contact
91% BSA apolar/total
SASA unbound
733 Ų
Apolar buried
492 Ų

Interaction summary

HB 3 HY 11 PI 3 CLASH 5

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

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank2.250Score-26.599
Inter norm-0.840Intra norm0.034
Top1000noExcludedno
Contacts18H-bonds3
Artifact reasongeometry warning; 14 clashes; 9 protein contact clashes; high strain Δ 48.2
Residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 GLU274 GLY199 GLY236 GLY237 GLY276 HIS197 HIS333 LYS69 PRO275 SER200 TYR331 TYR389

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap16Native recall0.84
Jaccard0.76RMSD-
HB strict1Strict recall0.11
HB same residue+role1HB role recall0.14
HB same residue2HB residue recall0.29

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
667 1.5018972035925722 -0.702622 -19.1165 6 12 0 0.00 0.00 - no Open
665 2.148044640714732 -0.875167 -27.3833 5 19 0 0.00 0.00 - no Open
674 2.250138561538429 -0.839896 -26.5988 3 18 16 0.84 0.14 - 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 -26.599kcal/mol
Ligand efficiency (LE) -0.8060kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.997
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 569.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.90
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 48.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 114.99kcal/mol
Minimised FF energy 66.77kcal/mol

SASA & burial

✓ computed
SASA (unbound) 733.4Ų
Total solvent-accessible surface area of free ligand
BSA total 542.6Ų
Buried surface area upon binding
BSA apolar 491.7Ų
Hydrophobic contacts buried
BSA polar 50.9Ų
Polar contacts buried
Fraction buried 74.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 90.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2721.1Ų
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 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1390.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)