FAIRMol

OHD_ACDS_41

Pose ID 8805 Compound 425 Pose 675

DB fairmolDocking 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_41
PDB1F3T↗

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
15.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.68, Jaccard 0.50, H-bond role recall 0.14
Burial
80%
Hydrophobic fit
97%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.790 kcal/mol/HA) ✓ Good fit quality (FQ -7.77) ✓ Good H-bonds (3 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (97%) ✗ Moderate strain (15.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-25.284
kcal/mol
LE
-0.790
kcal/mol/HA
Fit Quality
-7.77
FQ (Leeson)
HAC
32
heavy atoms
MW
572
Da
LogP
7.39
cLogP
Strain ΔE
15.3 kcal/mol
SASA buried
80%
Lipo contact
97% BSA apolar/total
SASA unbound
711 Ų
Apolar buried
555 Ų

Interaction summary

HB 3 HY 8 PI 4 CLASH 3

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 rank2.431Score-25.284
Inter norm-0.858Intra norm0.068
Top1000noExcludedno
Contacts20H-bonds3
Artifact reasongeometry warning; 13 clashes; 1 protein clash
Residues
ALA67 ARG154 ARG277 ASP332 GLU274 GLY199 GLY235 GLY236 GLY237 GLY276 HIS197 HIS333 LYS169 LYS69 PHE170 PHE196 SER167 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 overlap13Native recall0.68
Jaccard0.50RMSD-
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
670 0.7789096349661049 -1.06695 -32.7821 1 20 0 0.00 0.00 - no Open
669 0.8914987802842352 -0.865326 -25.1618 2 19 0 0.00 0.00 - no Open
670 2.3420972916200333 -0.878138 -26.4384 2 19 0 0.00 0.00 - no Open
675 2.430801341523712 -0.858318 -25.2837 3 20 13 0.68 0.14 - no Current
668 2.4586672432822207 -0.846475 -25.2036 2 19 0 0.00 0.00 - no Open
670 3.5081942563764814 -0.75017 -20.7342 3 12 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 -25.284kcal/mol
Ligand efficiency (LE) -0.7901kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.770
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 571.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 7.39
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 15.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 60.44kcal/mol
Minimised FF energy 45.10kcal/mol

SASA & burial

✓ computed
SASA (unbound) 710.7Ų
Total solvent-accessible surface area of free ligand
BSA total 572.2Ų
Buried surface area upon binding
BSA apolar 555.5Ų
Hydrophobic contacts buried
BSA polar 16.7Ų
Polar contacts buried
Fraction buried 80.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 97.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2693.9Ų
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 1433.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)