Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
20.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.38, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.632 kcal/mol/HA)
✓ Good fit quality (FQ -5.82)
✓ Good H-bonds (5 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ High strain energy (20.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-16.427
kcal/mol
LE
-0.632
kcal/mol/HA
Fit Quality
-5.82
FQ (Leeson)
HAC
26
heavy atoms
MW
351
Da
LogP
0.96
cLogP
Interaction summary
HB 5
HY 5
PI 0
CLASH 2
⚠ Exposure 41%
Interaction summary
HB 5
HY 5
PI 0
CLASH 2
⚠ Exposure 41%
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
Partial hydrophobic solvent exposure
41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 10
Exposed 7
LogP 0.96
H-bonds 5
Exposed fragments:
pyridyl (4/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 2.030 | Score | -16.427 |
|---|---|---|---|
| Inter norm | -0.847 | Intra norm | 0.216 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 5 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash; moderate strain Δ 20.0 | ||
| Residues |
ALA334
ARG242
ARG337
ASP243
ASP385
GLU384
GLY240
LEU339
PHE383
PRO338
SER282
THR241
VAL335
VAL336
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1NJJ | Contacts | 15 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG22
ARG242
ARG337
ARG342
ASP243
ASP385
GLN341
GLU384
LEU25
LEU339
LEU382
PRO340
PRO344
SER282
THR241
| ||
| Current overlap | 8 | Native recall | 0.53 |
| Jaccard | 0.38 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
Protein summary
398 residues
| Protein target | T14 | Atoms | 6140 |
|---|---|---|---|
| Residues | 398 | Chains | 1 |
| Residue summary | VAL: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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 246 | 0.05212297211422521 | -1.26728 | -31.9198 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 245 | 0.15333775693127674 | -1.28287 | -31.1967 | 11 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 251 | 0.375190949082224 | -1.10388 | -27.2108 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 269 | 2.030229846488461 | -0.847474 | -16.4266 | 5 | 14 | 8 | 0.53 | 0.20 | - | no | Current |
| 263 | 2.036323288363696 | -1.19848 | -25.4194 | 11 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 239 | 3.0498119327730224 | -1.07349 | -27.244 | 9 | 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.
Scoring & efficiency
Docking score
-16.427kcal/mol
Ligand efficiency (LE)
-0.6318kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.821
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
351.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.96
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.01kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
85.62kcal/mol
Minimised FF energy
65.61kcal/mol
SASA & burial
✓ computed
SASA (unbound)
629.9Ų
Total solvent-accessible surface area of free ligand
BSA total
478.3Ų
Buried surface area upon binding
BSA apolar
375.3Ų
Hydrophobic contacts buried
BSA polar
103.0Ų
Polar contacts buried
Fraction buried
75.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2423.8Ų
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
1398.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)