FAIRMol

OHD_TB2019_4

Pose ID 4792 Compound 2985 Pose 51

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
T08
T. brucei PTR1 T. brucei
Ligand OHD_TB2019_4
PDB6RX6↗

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
36.0 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.84, Jaccard 0.76, H-bond role recall 0.00
Burial
85%
Hydrophobic fit
90%
Reason: no major geometry red flags detected
2 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.014 kcal/mol/HA) ✓ Good fit quality (FQ -10.23) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (90%) ✗ Very high strain energy (36.0 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Many internal clashes (10)
Score
-35.508
kcal/mol
LE
-1.014
kcal/mol/HA
Fit Quality
-10.23
FQ (Leeson)
HAC
35
heavy atoms
MW
538
Da
LogP
1.68
cLogP
Strain ΔE
36.0 kcal/mol
SASA buried
85%
Lipo contact
90% BSA apolar/total
SASA unbound
780 Ų
Apolar buried
596 Ų

Interaction summary

HB 2 HY 24 PI 2 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 rank0.397Score-35.508
Inter norm-1.048Intra norm0.033
Top1000noExcludedno
Contacts18H-bonds2
Artifact reasongeometry warning; 10 clashes; 2 protein contact clashes; 1 severe cofactor-context clash; high strain Δ 36.0
Residues
ARG14 ASP161 GLY205 LEU208 LEU209 LEU263 MET163 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER95 TRP221 TYR174 TYR98 VAL206

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap16Native recall0.84
Jaccard0.76RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue2HB residue recall0.40

Protein summary

258 residues
Protein targetT08Atoms3881
Residues258Chains2
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

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:NAP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
51 0.39698825501507146 -1.04795 -35.5083 2 18 16 0.84 0.00 - no Current
45 1.3780897122946856 -0.598854 -19.9579 3 14 0 0.00 0.00 - no Open
49 2.9242297137967 -0.675491 -21.1975 2 18 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 -35.508kcal/mol
Ligand efficiency (LE) -1.0145kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.233
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 538.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.68
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 36.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 315.08kcal/mol
Minimised FF energy 279.03kcal/mol

SASA & burial

✓ computed
SASA (unbound) 779.9Ų
Total solvent-accessible surface area of free ligand
BSA total 659.5Ų
Buried surface area upon binding
BSA apolar 596.3Ų
Hydrophobic contacts buried
BSA polar 63.1Ų
Polar contacts buried
Fraction buried 84.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 90.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1842.5Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 926.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)